--- molphy-2.3b3.orig/debian/patches/src.diff +++ molphy-2.3b3/debian/patches/src.diff @@ -0,0 +1,667 @@ +diff -urbN src.orig/getseq.c src/getseq.c +--- src.orig/getseq.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/getseq.c 2006-09-10 16:19:56.000000000 +0200 +@@ -4,7 +4,7 @@ + */ + + #include "protml.h" +- ++#include "prot_tml.h" + + void + getsize(ifp, maxspc, numsite, commentp) +@@ -18,7 +18,7 @@ + + if (fgets(line, BUFLINE, ifp) != NULL) { + if (sscanf(line, "%d %d", maxspc, numsite) == 2) { +- for (cp = line; isdigit(*cp) || isspace(*cp) && *cp != '\0'; cp++) ++ for (cp = line; isdigit(*cp) || isspace(*cp) /*&& *cp != '\0'*/; cp++) + ; + *commentp = new_cvector(strlen(cp) + 1); + if (*cp != '\0') { +diff -urbN src.orig/Makefile src/Makefile +--- src.orig/Makefile 1996-07-02 16:56:36.000000000 +0200 ++++ src/Makefile 2006-09-10 16:19:56.000000000 +0200 +@@ -1,10 +1,13 @@ +-INSTALLDIR = ./.. # /usr/local/bin/molphy ++.SUFFIXES: .o .c ++ ++INSTALLDIR = /usr/local/bin/molphy + + CC = gcc # cc, gcc, c89 +-CFLAGS = -O # -O4 or +O ++CFLAGS = -O3 # -O4 or +O + DEFINE = # +-LIBS = -lm # -lM +-CP = cp # copy command ++LIBS = -lm -lc ++# CP = cp -a ++CP = ln -s + NUCLE = -DNUC + NJLE = -DNJ + SDLE = -DSD +@@ -82,102 +85,102 @@ + + # protml nucml + +-protml.o : protml.c protml.h molphy.h ++protml.o : protml.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c protml.c + Nucml.c : protml.c optimtpm.c abratio.c + $(CP) protml.c Nucml.c +-Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c ++Nucml.o : Nucml.c protml.h molphy.h optimtpm.c abratio.c matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucml.c +-getseq.o : getseq.c protml.h molphy.h ++getseq.o : getseq.c protml.h molphy.h prot_tml.h + $(CC) $(CFLAGS) $(DEFINE) -c getseq.c +-seqproc.o : seqproc.c protml.h molphy.h ++seqproc.o : seqproc.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c seqproc.c +-tranprb.o : tranprb.c protml.h molphy.h ++tranprb.o : tranprb.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c tranprb.c + Ntranprb.c : tranprb.c + $(CP) tranprb.c Ntranprb.c +-Ntranprb.o : Ntranprb.c protml.h molphy.h ++Ntranprb.o : Ntranprb.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ntranprb.c +-distan.o : distan.c protml.h molphy.h ++distan.o : distan.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c distan.c + Ndistan.c : distan.c + $(CP) distan.c Ndistan.c +-Ndistan.o : Ndistan.c protml.h molphy.h ++Ndistan.o : Ndistan.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Ndistan.c +-mltree.o : mltree.c protml.h molphy.h ++mltree.o : mltree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c mltree.c +-altree.o : altree.c protml.h molphy.h ++altree.o : altree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c altree.c +-qltree.o : qltree.c protml.h molphy.h ++qltree.o : qltree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c qltree.c +-sltree.o : sltree.c protml.h molphy.h ++sltree.o : sltree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c sltree.c +-njtree.o : njtree.c protml.h molphy.h ++njtree.o : njtree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c njtree.c +-njmtree.o : njmtree.c protml.h molphy.h ++njmtree.o : njmtree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c njmtree.c +-mlklhd.o : mlklhd.c protml.h molphy.h ++mlklhd.o : mlklhd.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c mlklhd.c + Nmlklhd.c : mlklhd.c + $(CP) mlklhd.c Nmlklhd.c +-Nmlklhd.o : Nmlklhd.c protml.h molphy.h ++Nmlklhd.o : Nmlklhd.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nmlklhd.c +-prtree.o : prtree.c protml.h molphy.h ++prtree.o : prtree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c prtree.c +-pstree.o : pstree.c protml.h molphy.h ++pstree.o : pstree.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c pstree.c + +-protproc.o : protproc.c protml.h molphy.h ++protproc.o : protproc.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c protproc.c +-nucproc.o : nucproc.c protml.h molphy.h ++nucproc.o : nucproc.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c nucproc.c +-dyhfjtt.o : dyhfjtt.c protml.h molphy.h ++dyhfjtt.o : dyhfjtt.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c dyhfjtt.c +-mtrev24.o : mtrev24.c protml.h molphy.h ++mtrev24.o : mtrev24.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c mtrev24.c + + # protst nucst + +-protst.o : protst.c protst.h molphy.h ++protst.o : protst.c protst.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c protst.c + Nucst.c : protst.c + $(CP) protst.c Nucst.c +-Nucst.o : Nucst.c protst.h molphy.h ++Nucst.o : Nucst.c protst.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nucst.c + +-seqstat.o : seqstat.c protst.h molphy.h ++seqstat.o : seqstat.c protst.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c seqstat.c + Nseqstat.c : seqstat.c + $(CP) seqstat.c Nseqstat.c +-Nseqstat.o : Nseqstat.c protst.h molphy.h ++Nseqstat.o : Nseqstat.c protst.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(NUCLE) $(DEFINE) -c Nseqstat.c + + # tridist njdist + +-tridist.o : tridist.c tridist.h molphy.h ++tridist.o : tridist.c tridist.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c tridist.c +-triproc.o : triproc.c tridist.h molphy.h ++triproc.o : triproc.c tridist.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c triproc.c + Njdist.c : tridist.c + $(CP) tridist.c Njdist.c +-Njdist.o : Njdist.c tridist.h molphy.h ++Njdist.o : Njdist.c tridist.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Njdist.c +-njproc.o : njproc.c tridist.h molphy.h ++njproc.o : njproc.c tridist.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c njproc.c + sddist.o : sddist.c sddist.h molphy.h + $(CC) $(CFLAGS) $(DEFINE) $(SDLE) -c sddist.c + sdproc.o : sdproc.c sddist.h molphy.h + $(CC) $(CFLAGS) $(DEFINE) -c sdproc.c +-distproc.o : distproc.c tridist.h molphy.h ++distproc.o : distproc.c tridist.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c distproc.c + Dpstree.c : pstree.c + $(CP) pstree.c Dpstree.c +-Dpstree.o : Dpstree.c tridist.h molphy.h ++Dpstree.o : Dpstree.c tridist.h molphy.h protml.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) $(NJLE) -c Dpstree.c + + # totalml + +-totalml.o : totalml.c totalml.h molphy.h ++totalml.o : totalml.c totalml.h molphy.h matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c totalml.c + + # tmlprot +@@ -192,11 +195,11 @@ + + Prottpm.c : protml.c + $(CP) protml.c Prottpm.c +-Prottpm.o : Prottpm.c protml.h molphy.h ++Prottpm.o : Prottpm.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) -DTPM $(DEFINE) -c Prottpm.c + Nuctpm.c : protml.c + $(CP) protml.c Nuctpm.c +-Nuctpm.o : Nuctpm.c protml.h molphy.h ++Nuctpm.o : Nuctpm.c protml.h molphy.h matrixut.h + $(CC) $(CFLAGS) -DTPM $(NUCLE) $(DEFINE) -c Nuctpm.c + + tpmproc.o : tpmproc.c protml.h molphy.h +@@ -234,11 +237,12 @@ + + matrixut.o : matrixut.c matrixut.h + $(CC) $(CFLAGS) $(DEFINE) -c matrixut.c +-mygetopt.o : mygetopt.c ++mygetopt.o : mygetopt.c molphy.h + $(CC) $(CFLAGS) $(DEFINE) -c mygetopt.c + + install : $(PRGS) +- $(CP) $(PRGS) $(INSTALLDIR) ++ mkdir -p $(INSTALLDIR) ++ cp -a $(PRGS) $(INSTALLDIR) + cd $(INSTALLDIR); \ + chmod 755 $(PRGS) + +@@ -272,6 +276,15 @@ + rcp [a-z]*.c *.h Makefile sunmh:/home/sunmh/adachi/work/molphybeta + + RMSRC : +- rm bdate.c compcrit.c dmlproc.c protdml.c protdml.h ptnlkl.c \ +- sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c tpmproc.c \ ++# rm bdate.c compcrit.c protdml.h ptnlkl.c \ ++# sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \ ++# triadml.c ++ @echo This target intends to remove the following files ++ @echo bdate.c compcrit.c protdml.h ptnlkl.c \ ++ sddist.c sddist.h sdproc.c tmlprot.c tmlprot.h tpgraph.c \ + triadml.c ++ @echo This is prevented because I consider it to be a bad idea to remove sources. ++ ++## The following file is unused in original molphy and there are just plain ++## dependencies in the arb pachage because it was automatically generated ++## mtrev22.o: protml.h molphy.h matrixut.h +diff -urbN src.orig/molphy.h src/molphy.h +--- src.orig/molphy.h 1996-07-02 16:56:01.000000000 +0200 ++++ src/molphy.h 2006-09-10 16:19:56.000000000 +0200 +@@ -17,7 +17,7 @@ + #define DIR_CHAR '/' /* directory separator '/' (UNIX) */ + #else + #define SW_CHAR '/' /* switch charcter '/' (MSDOS) */ +-#define DIR_CHAR '\' /* directory separator '\' (MSDOS) */ ++#define DIR_CHAR '\\' /* directory separator '\' (MSDOS) */ + #endif + + #ifdef RAND_MAX +diff -urbN src.orig/nucproc.c src/nucproc.c +--- src.orig/nucproc.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/nucproc.c 2006-09-10 16:19:56.000000000 +0200 +@@ -20,9 +20,7 @@ + }; + + +-int +-isacid(c) +-char c; ++int isacid(char c) + { + /* nuc */ + switch (c) { +diff -urbN src.orig/protml.c src/protml.c +--- src.orig/protml.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/protml.c 2006-09-10 16:36:01.000000000 +0200 +@@ -1124,6 +1124,7 @@ + prtopology(Ctree); + resulttree(Ctree); + pstree(Epsfp, Ctree); ++ fputcphylogeny(Trefp, Ctree); + FREE_LPMATRIX(Lklptrn); + + } else if (Njoin_optn) { /* NJ MODE */ +diff -urbN src.orig/protst.c src/protst.c +--- src.orig/protst.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/protst.c 2006-09-10 16:19:56.000000000 +0200 +@@ -136,31 +136,31 @@ + } + + +-#if 0 +-void +-header(ofp, maxspc, numsite, commentp) +-FILE *ofp; +-int *maxspc; +-int *numsite; +-char **commentp; +-{ +- time_t ct; +- char *datetime, *ip, *jp; +- +- fprintf(ofp, "%s %s ", Prog_name, VERSION); +- +- ct = time(NULL); +- datetime = ctime(&ct); +- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; +- *ip = '\0'; +- fputs(datetime + 4, ofp); +- fputs(" ", ofp); +- fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp); +- free_cvector(*commentp); +-} /*_ header */ +-#endif ++/* #if 0 */ ++/* void */ ++/* header(ofp, maxspc, numsite, commentp) */ ++/* FILE *ofp; */ ++/* int *maxspc; */ ++/* int *numsite; */ ++/* char **commentp; */ ++/* { */ ++/* time_t ct; */ ++/* char *datetime, *ip, *jp; */ ++ ++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */ ++ ++/* ct = time(NULL); */ ++/* datetime = ctime(&ct); */ ++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */ ++/* *ip = '\0'; */ ++/* fputs(datetime + 4, ofp); */ ++/* fputs(" ", ofp); */ ++/* fprintf(ofp, " %d OTUs %d sites %s\n", *maxspc, *numsite, *commentp); */ ++/* free_cvector(*commentp); */ ++/* } / *_ header * / */ ++/* #endif */ + +-void ++ void + header(ofp, maxspc, numsite, commentp) + FILE *ofp; + int *maxspc; +diff -urbN src.orig/prot_tml.h src/prot_tml.h +--- src.orig/prot_tml.h 1970-01-01 01:00:00.000000000 +0100 ++++ src/prot_tml.h 2006-09-10 16:19:56.000000000 +0200 +@@ -0,0 +1,241 @@ ++#ifndef P_ ++# if defined(__STDC__) || defined(__cplusplus) ++# define P_(s) s ++# else ++# define P_(s) () ++# endif ++#else ++# error P_ already defined elsewhere ++#endif ++ ++ ++/* getseq.c */ ++void getsize P_((FILE *ifp, int *maxspc, int *numsite, char **commentp)); ++void getid P_((FILE *ifp, char **identif, char **sciname, char **engname, int *nl, int *notu)); ++void getsites P_((FILE *ifp, cmatrix seqchar, int numsite, int *nl, int *notu)); ++void getseq P_((FILE *ifp, char **identif, char **sciname, char **engname, cmatrix seqchar, int maxspc, int numsite)); ++void getidsites P_((FILE *ifp, cmatrix identif, cmatrix seqchar, int numsite, int *nl, int *notu)); ++void getseqs P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite)); ++void getseqi P_((FILE *ifp, char **identif, cmatrix seqchar, int maxspc, int numsite)); ++void fputid P_((FILE *ofp, char *name, int maxcolumn)); ++void prsequence P_((FILE *ofp, char **identif, char **seqchar, int maxspc, int maxsite)); ++ ++/* seqproc.c */ ++void convseq P_((imatrix seqconint, int maxspc, int numptrn)); ++void getfreqepm P_((cmatrix seqchar, double *freqemp, int maxspc, int maxsite)); ++void convfreq P_((double *freqemp)); ++void radixsort P_((cmatrix seqchar, ivector alias, int maxspc, int maxsite, int *numptrn)); ++void condenceseq P_((cmatrix seqchar, ivector alias, imatrix seqconint, ivector weight, int maxspc, int maxsite, int numptrn)); ++void getnumsites P_((imatrix seqconint, ivector numsites, ivector weight, int numspc, int numptrn)); ++void prcondenceseq P_((char **identif, imatrix seqconint, ivector weight, int numspc, int numsite, int numptrn)); ++ ++/* mltree.c */ ++Node **new_npvector P_((int n)); ++void free_npvector P_((Node **v)); ++Tree *new_tree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint)); ++int getbuftree P_((int numspc, cmatrix identif)); ++void changedistan P_((dmatrix distanmat, dvector distanvec, int numspc)); ++void getproportion P_((double *proportion, dvector distanvec, int maxpair)); ++Infotree *newinfotrees P_((int numtree, int buftree)); ++Infoaltree *newinfoaltrees P_((int numaltree, int buftree)); ++void getnumtree P_((FILE *ifp, int *numtree)); ++void getusertree P_((FILE *ifp, cvector strtree, int buftree)); ++Node *internalnode P_((Tree *tr, char **cpp, int *ninode, char *st)); ++void constructtree P_((Tree *tr, cvector strtree)); ++void prcurtree P_((Tree *tr)); ++void pathing P_((Tree *tr)); ++void lslength P_((Tree *tr, dvector distanvec, int numspc)); ++void slslength P_((Tree *tr, dmatrix dmat, int ns)); ++void fmlength P_((Tree *tr, dmatrix dmat, int ns)); ++void resulttree P_((Tree *tr)); ++void bootstrap P_((Infotree *infotrs, LPMATRIX lklptrn)); ++void tabletree P_((Infotree *infotrs, LPMATRIX lklptrn)); ++void tableinfo P_((Infotree *infotrs)); ++void rerootq P_((Tree *tr, int numspc)); ++void outlklhd P_((LPMATRIX lklptrn)); ++void putsortseq P_((Tree *tr)); ++ ++/* altree.c */ ++Tree *new_atree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint)); ++Node *new_dnode P_((void)); ++Node *new_anode P_((void)); ++Node ***new_nodematrix P_((int nrow, int ncol)); ++void free_nodematrix P_((Node ***m)); ++void aproxlkl P_((Tree *tr)); ++void aproxlkl P_((Tree *tr)); ++void praproxlkl P_((Tree *tr)); ++void aproxtree P_((Tree *tr, int ntr)); ++void wedge P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder, Node *op)); ++void autoconstruction P_((Tree *tr, int onode, Node **poolnode, Node **addposition, ivector poolorder)); ++Node *inbranode P_((Tree *tr, char **cpp, int *nenode, int numorder, Node ***poolnode2, cvector st)); ++void streeinit P_((Tree *tr, cvector strtree, Node **poolnode, Node **addposition, ivector poolorder)); ++void atreeinit P_((Tree *tr, Node **poolnode, Node **addposition, ivector poolorder)); ++void tablealtree P_((int nt)); ++ ++/* qltree.c */ ++Infoqltree *newinfoqltrees P_((int n, int maxbrnch)); ++Infoaddtree *newinfoaddtree P_((int buftree)); ++void initturn P_((Tree *tr)); ++void randturn P_((Tree *tr)); ++void convertdistan P_((Tree *tr, int numspc, dmatrix distanmat, dvector distanvec)); ++void praproxlkl2 P_((FILE *fp, Tree *tr)); ++int addotu P_((Tree *tr, Node *cp, Node *np, Node *ip, int cnspc)); ++int addotual P_((Tree *tr, Node *cp, Node *np, Node *ip, dvector lengs)); ++void roundtree P_((Tree *tr, int cnspc, Infoqltree *infoqltrees, Infoqltree *qhead, Infoqltree *qtail)); ++void qtreeinit P_((Tree *tr)); ++void tableaddtree P_((Infoaddtree *head, int numaddtree)); ++ ++/* sltree.c */ ++Tree *new_stree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint)); ++Infosltree *newinfosltrees P_((int num, int maxbrnch)); ++void insertbranch P_((Node *ibp, Node *np)); ++void deletebranch P_((Node *ibp, Node *np)); ++void movebranch P_((Node *jbp, Node *ip)); ++void removebranch P_((Node *jbp, Node *ip)); ++void subpathing P_((Node *np)); ++void copylength P_((Tree *tr, dvector lengs)); ++Node *sdml P_((Tree *tr, Node *op)); ++void decomposition P_((Tree *tr, int n, Infosltree *infosltrees)); ++void stardecomp P_((Tree *tr, int maxibrnch)); ++dcube new_dcubesym P_((int nrow, int ncol)); ++void free_dcubesym P_((dcube c)); ++void ystardecomp P_((Tree *tr)); ++void xstardecomp P_((Tree *tr)); ++ ++/* njtree.c */ ++Tree *new_njtree P_((int maxspc, int maxibrnch, int numptrn, imatrix seqconint)); ++void free_njtree P_((Tree *tr, int maxspc, int maxibrnch)); ++double emledis P_((double dis, Node *ip, Node *kp)); ++double imledis P_((double dis, Node *ip, Node *kp)); ++void redmat P_((dmatrix dmat, double dij, Node **psotu, ivector otu, int restsp, int ii, int jj, int ns)); ++void enjtree P_((Tree *tr, dmatrix distan, int ns, boolean flag)); ++ ++/* njmtree.c */ ++void initsubplkl P_((Node *op)); ++void mlepartlen P_((Node *ip, Node *jp, Node **rotup, int nr, int ns)); ++void remldmat P_((dmatrix dmat, double dij, Node **psotu, Node **rotup, int otui, int otuj, int ns)); ++void njmtree P_((Tree *tr, dmatrix distan, int ns, boolean flag)); ++ ++/* prtree.c */ ++void putctopology P_((Tree *tr)); ++void fputctopology P_((FILE *fp, Tree *tr)); ++void fputcphylogeny P_((FILE *fp, Tree *tr)); ++void prtopology P_((Tree *tr)); ++void strctree P_((Tree *tr, char *ltree)); ++ ++/* pstree.c */ ++void psdicter P_((FILE *fp)); ++void pstree P_((FILE *fp, Tree *tr)); ++ ++/* matrixut.c */ ++void maerror P_((char *message)); ++fvector new_fvector P_((int n)); ++fmatrix new_fmatrix P_((int nrow, int ncol)); ++fcube new_fcube P_((int ntri, int nrow, int ncol)); ++void free_fvector P_((fvector v)); ++void free_fmatrix P_((fmatrix m)); ++void free_fcube P_((fcube c)); ++dvector new_dvector P_((int n)); ++dmatrix new_dmatrix P_((int nrow, int ncol)); ++dcube new_dcube P_((int ntri, int nrow, int ncol)); ++void free_dvector P_((dvector v)); ++void free_dmatrix P_((dmatrix m)); ++void free_dcube P_((dcube c)); ++cvector new_cvector P_((int n)); ++cmatrix new_cmatrix P_((int nrow, int ncol)); ++ccube new_ccube P_((int ntri, int nrow, int ncol)); ++void free_cvector P_((cvector v)); ++void free_cmatrix P_((cmatrix m)); ++void free_ccube P_((ccube c)); ++ivector new_ivector P_((int n)); ++imatrix new_imatrix P_((int nrow, int ncol)); ++icube new_icube P_((int ntri, int nrow, int ncol)); ++void free_ivector P_((ivector v)); ++void free_imatrix P_((imatrix m)); ++void free_icube P_((icube c)); ++ ++/* mygetopt.c */ ++int mygetopt P_((int argc, char **argv, char *optstring)); ++ ++/* protml.c */ ++void copyright P_((void)); ++void usage P_((void)); ++void helpinfo P_((void)); ++int main P_((int argc, char **argv)); ++void header P_((FILE *ofp, int *maxspc, int *numsite, char **commentp)); ++void headerd P_((FILE *ofp, int *maxspc, int *numsite, char **commentp)); ++void pml P_((FILE *ifp, FILE *ofp)); ++ ++/* protproc.c */ ++int isacid P_((int c)); ++int acid2int P_((int c)); ++char acid2chint P_((int c)); ++char chint2acid P_((int c)); ++char int2acid P_((int i)); ++ ++/* dyhfjtt.c */ ++void dyhfjtt P_((dmattpmty r, double *f, boolean flag)); ++ ++/* mtrev24.c */ ++void mtrev P_((dmattpmty r, double *f)); ++ ++/* tranprb.c */ ++void elmhes P_((dmattpmty a, int *ordr, int n)); ++void eltran P_((dmattpmty a, dmattpmty zz, int *ordr, int n)); ++void hqr2 P_((int n, int low, int hgh, int *err, dmattpmty h, dmattpmty zz, double *wr, double *wi)); ++void readrsrf P_((dmattpmty r, dvectpmty f, int n)); ++void tpmonepam P_((dmattpmty a, double *f)); ++void luinverse P_((dmattpmty omtrx, dmattpmty imtrx, int size)); ++void mproduct P_((dmattpmty am, dmattpmty bm, dmattpmty cm, int na, int nb, int nc)); ++void preigen P_((void)); ++void checkevector P_((dmattpmty imtrx, int nn)); ++void getrsr P_((dmattpmty a, dvectpmty ftpm)); ++void tranprobmat P_((void)); ++void varitpm P_((void)); ++void prfreq P_((void)); ++void tprobmtrx P_((double arc, dmattpmty tpr)); ++void tprobmtrxt P_((double arc, dmattpmty tpr)); ++void tdiffmtrx P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2)); ++void tprobmtrx2 P_((double arc, dmattpmty tpr)); ++void tdiffmtrx2 P_((double arc, dmattpmty tpr, dmattpmty td1, dmattpmty td2)); ++ ++/* distan.c */ ++void distance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite)); ++void lddistance P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite)); ++void tdistan P_((ivector seqi, ivector seqj, dmatrix probk, ivector weight, int nptrn, double *len, double *lvari, dcube triprob)); ++void tdistan2 P_((ivector seqi, ivector seqj, ivector seqk, ivector seqw, int nsite, double *len, double *lvari, dcube triprob)); ++void tridistance P_((dmatrix distanmat, imatrix seqconint, ivector weight, int maxspc, int numptrn)); ++void tridistance2 P_((dmatrix distanmat, cmatrix seqchar, int maxspc, int numsite)); ++void putdistance P_((cmatrix identif, cmatrix sciname, cmatrix engname, dmatrix distanmat, int maxspc)); ++void checkseq P_((imatrix seqconint, int maxspc, int numptrn)); ++ ++/* mlklhd.c */ ++double probnormal P_((double z)); ++double uprobnormal P_((double z)); ++void copypart1 P_((Node *op, Node *cp)); ++void prodpart1 P_((Node *op, Node *cp)); ++void prodpart P_((Node *op)); ++void partilkl P_((Node *op)); ++void partelkl P_((Node *op)); ++void partelkl2 P_((Node *op)); ++void initpartlkl P_((Tree *tr)); ++void regupartlkl P_((Tree *tr)); ++void mlibranch P_((Node *op, double eps, int nloop)); ++void mlebranch P_((Node *op, double eps, int nloop)); ++void mlebranch2 P_((Node *op, double eps, int nloop)); ++void evallkl P_((Node *op)); ++Node *mlikelihood P_((Tree *tr)); ++void ribranch P_((Node *op)); ++Node *relibranch P_((Node *op)); ++void mlvalue P_((Tree *tr, Infotree *infotrs)); ++void reroot P_((Tree *tr, Node *rp)); ++void sorttree P_((Tree *tr, Node *rp)); ++void chroot P_((Tree *tr, int s1, int s2)); ++void noexch P_((Node *rp, ivector exchstate)); ++void reliml P_((Tree *tr, Node *op, double lklorg, LPVECTOR mlklptrn, double *rel)); ++void localbp P_((dmatrix reliprob, LPVECTOR mlklptrn, LPCUBE rlklptrn, ivector whichml, int nb, int ns)); ++void reliabranch P_((Tree *tr)); ++void annealing P_((Tree *tr)); ++void qlrsearch P_((Tree *tr)); ++ ++#undef P_ +diff -urbN src.orig/pstree.c src/pstree.c +--- src.orig/pstree.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/pstree.c 2006-09-10 16:19:56.000000000 +0200 +@@ -153,10 +153,10 @@ + if (len == 0) len = 1; + if (cp->descen) x += len; + if (cp->isop == NULL) { /* external node */ +- (Sciname[cp->num][0] != '\0') ? ++ (Sciname[cp->num] && Sciname[cp->num][0] != '\0') ? /* @@@OLIVER */ + (name = Sciname[cp->num]) : (name = Identif[cp->num]); + s = (int)(fontw * (strlen(name) + 1) + 10); +- if (Engname[cp->num][0] != '\0') { ++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */ + s += (int)(fontw * (strlen(Engname[cp->num]) + 1)); + } + xs = x + s; +@@ -232,12 +232,12 @@ + fprintf(fp, "n %3d %3d m %3d %3d l s ", x - len, y, x, y); + fprintf(fp, " %3d %3d m", x + (int)fontw, y-fontc); + fprintf(fp, " %% %3d\n", cp->num+1); +- if (Sciname[cp->num][0] == '\0') { ++ if (Sciname[cp->num]== 0 || Sciname[cp->num][0] == '\0') { /* @@@OLIVER */ + fprintf(fp, " Fid ff %d sf (%s) sh", fonts, Identif[cp->num]); + } else { + fprintf(fp, " Fsc ff %d sf (%s) sh", fonts, Sciname[cp->num]); + } +- if (Engname[cp->num][0] != '\0') { ++ if (Engname[cp->num] && Engname[cp->num][0] != '\0') { /* @@@OLIVER */ + fprintf(fp, " Fid ff %d sf ( %s) sh\n",fonts,Engname[cp->num]); + } else { + fprintf(fp, "\n"); +diff -urbN src.orig/qltree.c src/qltree.c +--- src.orig/qltree.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/qltree.c 2006-09-10 16:19:56.000000000 +0200 +@@ -140,7 +140,7 @@ + } /*_ praproxlkl2 */ + + +-addotu(tr, cp, np, ip, cnspc) ++int addotu(tr, cp, np, ip, cnspc) + Tree *tr; + Node *cp, *np, *ip; + int cnspc; +diff -urbN src.orig/totalml.c src/totalml.c +--- src.orig/totalml.c 1996-07-02 16:56:00.000000000 +0200 ++++ src/totalml.c 2006-09-10 16:19:56.000000000 +0200 +@@ -40,31 +40,31 @@ + } + + +-#if 0 +-void +-header(ofp, numseqs, allsite, commentp) +-FILE *ofp; +-int *numseqs; +-int *allsite; +-char **commentp; +-{ +- time_t ct; +- char *datetime, *ip, *jp; ++/* #if 0 */ ++/* void */ ++/* header(ofp, numseqs, allsite, commentp) */ ++/* FILE *ofp; */ ++/* int *numseqs; */ ++/* int *allsite; */ ++/* char **commentp; */ ++/* { */ ++/* time_t ct; */ ++/* char *datetime, *ip, *jp; */ ++ ++/* fprintf(ofp, "%s %s ", Prog_name, VERSION); */ ++ ++/* ct = time(NULL); */ ++/* datetime = ctime(&ct); */ ++/* for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; */ ++/* *ip = '\0'; */ ++/* fputs(datetime + 4, ofp); */ ++/* fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite); */ ++/* / * fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); * / */ ++/* } / *_ header * / */ ++/* #endif */ + +- fprintf(ofp, "%s %s ", Prog_name, VERSION); + +- ct = time(NULL); +- datetime = ctime(&ct); +- for (ip = datetime+11, jp = datetime+20; *jp != '\n'; ) *ip++ = *jp++; +- *ip = '\0'; +- fputs(datetime + 4, ofp); +- fprintf(ofp, " %d data %d sites.\n", *numseqs, *allsite); +-/* fprintf(ofp, " %d data %d sites. %s\n", *numseqs, *allsite, *commentp); */ +-} /*_ header */ +-#endif +- +- +-void ++ void + header(ofp, maxspc, numsite, commentp) + FILE *ofp; + int *maxspc; --- molphy-2.3b3.orig/debian/patches/utl_Install.diff +++ molphy-2.3b3/debian/patches/utl_Install.diff @@ -0,0 +1,8 @@ +--- utl/Install.orig 1996-07-02 16:56:02.000000000 +0200 ++++ utl/Install 2006-09-10 15:20:27.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + + # Usage: Install install_directory + --- molphy-2.3b3.orig/debian/tests/compare/README.compare +++ molphy-2.3b3/debian/tests/compare/README.compare @@ -0,0 +1,13 @@ +I've got those test examples from + http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/testdata +The original files in the compare directory where build with molphy 2.2. +I found out that the results with version 2.3b3 differ slightly in +the precision of some floats. I think this is OK. + +On the other hand there were some different trees created in + test4.nj, test6.mls, test7.mls and test15.nj +So I leave here the original example file named -2.2 and just +leave it to some more educated people in phylogenetic trees to decide what´s +correct here. In my opinion this are just different representations +of one tree but please report it to if you doubt that. + --- molphy-2.3b3.orig/debian/tests/compare/test15.dis +++ molphy-2.3b3/debian/tests/compare/test15.dis @@ -0,0 +1,61 @@ +15 409 sites JTT test15.ptn +Homo + 0.000000000000 0.036941950975 0.151849499085 0.175452276938 0.186308284045 + 0.178557231654 0.175460021426 0.171381705808 0.242558390091 0.239818426034 + 0.711229145466 0.627975207365 0.657474744501 0.681818041556 0.738465099336 +Xenopus + 0.036941950975 0.000000000000 0.164701173415 0.190703594342 0.197551671507 + 0.184308599151 0.182349699549 0.164080100858 0.255776516678 0.244680817390 + 0.715551867177 0.644715916524 0.649699323398 0.692484941077 0.756225268778 +Drosophil + 0.151849499085 0.164701173415 0.000000000000 0.125772039669 0.215277763145 + 0.211175855041 0.227217806440 0.204178994811 0.256220603581 0.255322597474 + 0.719922660503 0.628402341913 0.635238587361 0.650765472456 0.728333862467 +Artemia + 0.175452276938 0.190703594342 0.125772039669 0.000000000000 0.216896015811 + 0.222175650450 0.247563133706 0.219781287346 0.273666339087 0.290368846607 + 0.764658513106 0.661840294620 0.694883040771 0.665517479246 0.744690215581 +Saccharom + 0.186308284045 0.197551671507 0.215277763145 0.216896015811 0.000000000000 + 0.091449159965 0.160750248794 0.145644518755 0.280385638946 0.278657537403 + 0.733098885492 0.643129634435 0.664012590502 0.693115324686 0.754796557471 +Candida + 0.178557231654 0.184308599151 0.211175855041 0.222175650450 0.091449159965 + 0.000000000000 0.138031643786 0.122675348331 0.273008128171 0.278020382072 + 0.713140264266 0.625663809960 0.657954595852 0.683280435752 0.745473130516 +Mucor + 0.175460021426 0.182349699549 0.227217806440 0.247563133706 0.160750248794 + 0.138031643786 0.000000000000 0.072991018602 0.271991858303 0.272704035853 + 0.729075758693 0.676155341917 0.671334562854 0.699499598663 0.773928364495 +Absidia + 0.171381705808 0.164080100858 0.204178994811 0.219781287346 0.145644518755 + 0.122675348331 0.072991018602 0.000000000000 0.261401901747 0.259659630766 + 0.714834621911 0.648508655180 0.643308824691 0.676862516776 0.764373341245 +Arabidops + 0.242558390091 0.255776516678 0.256220603581 0.273666339087 0.280385638946 + 0.273008128171 0.271991858303 0.261401901747 0.000000000000 0.031785685549 + 0.750900038825 0.671512195407 0.693073592410 0.730190796496 0.792617210957 +Lycopersi + 0.239818426034 0.244680817390 0.255322597474 0.290368846607 0.278657537403 + 0.278020382072 0.272704035853 0.259659630766 0.031785685549 0.000000000000 + 0.745732191534 0.659295620612 0.674320313265 0.720433145071 0.789316205974 +Sulpholob + 0.711229145466 0.715551867177 0.719922660503 0.764658513106 0.733098885492 + 0.713140264266 0.729075758693 0.714834621911 0.750900038825 0.745732191534 + 0.000000000000 0.576508504143 0.604648603433 0.694265147576 0.741009725023 +Thermococ + 0.627975207365 0.644715916524 0.628402341913 0.661840294620 0.643129634435 + 0.625663809960 0.676155341917 0.648508655180 0.671512195407 0.659295620612 + 0.576508504143 0.000000000000 0.493086506111 0.523696929224 0.538544990613 +Thermopla + 0.657474744501 0.649699323398 0.635238587361 0.694883040771 0.664012590502 + 0.657954595852 0.671334562854 0.643308824691 0.693073592410 0.674320313265 + 0.604648603433 0.493086506111 0.000000000000 0.512104690742 0.559086291661 +Methanoco + 0.681818041556 0.692484941077 0.650765472456 0.665517479246 0.693115324686 + 0.683280435752 0.699499598663 0.676862516776 0.730190796496 0.720433145071 + 0.694265147576 0.523696929224 0.512104690742 0.000000000000 0.515261390739 +Halobacte + 0.738465099336 0.756225268778 0.728333862467 0.744690215581 0.754796557471 + 0.745473130516 0.773928364495 0.764373341245 0.792617210957 0.789316205974 + 0.741009725023 0.538544990613 0.559086291661 0.515261390739 0.000000000000 --- molphy-2.3b3.orig/debian/tests/compare/test15.ml +++ molphy-2.3b3/debian/tests/compare/test15.ml @@ -0,0 +1,150 @@ +protml 2.3b3 (11/09/01) JTT-F 15 OTUs 409 sites. test15.ptn +#1 + :-1 Homo + :--16 + : :-2 Xenopus + :-18 + : : :--3 Drosophil + : :--17 + : :---4 Artemia + :---22 + : : :--5 Saccharom + : : :--19 + : : : :--6 Candida + : :--21 + : : :--7 Mucor + : :--20 + : :-8 Absidia +:----------24 +: : :-9 Arabidops +: :----23 +: :-10 Lycopersi +: +:------------11 Sulpholob +: +: :-------12 Thermococ +:----27 + : :---------13 Thermopla + :---26 + : :---------14 Methanoco + :----25 + :----------15 Halobacte + +No.1 ext. branch S.E. int. branch S.E. +Homo 1 1.25 0.64 16 5.33 1.31 +Xenopus 2 2.52 0.84 17 6.10 1.39 +Drosophil 3 4.11 1.12 18 1.67 0.87 +Artemia 4 8.65 1.57 19 3.57 1.11 +Saccharom 5 5.45 1.29 20 4.99 1.30 +Candida 6 3.91 1.12 21 5.24 1.37 +Mucor 7 5.03 1.21 22 6.34 1.69 +Absidia 8 2.69 0.93 23 12.06 2.14 +Arabidops 9 2.07 0.76 24 29.94 3.79 +Lycopersi 10 1.17 0.60 25 10.56 2.30 +Sulpholob 11 37.09 4.11 26 6.32 2.10 +Thermococ 12 20.28 2.95 27 10.49 2.45 +Thermopla 13 25.06 3.19 TBL : 275.20 iter: 6 +Methanoco 14 25.01 3.27 ln L: -5932.72 +- 198.62 +Halobacte 15 28.29 3.46 AIC : 11957.43 +#2 + :-1 Homo + :--16 + : :-2 Xenopus + :-18 + : : :--3 Drosophil + : :--17 + : :---4 Artemia +:------------24 +: : :--5 Saccharom +: : :--19 +: : : :--6 Candida +: : :--21 +: : : : :--7 Mucor +: : : :--20 +: : : :-8 Absidia +: :-23 +: : :-9 Arabidops +: :------22 +: :-10 Lycopersi +: +:------------11 Sulpholob +: +: :-------12 Thermococ +:----27 + : :---------13 Thermopla + :---26 + : :---------14 Methanoco + :----25 + :----------15 Halobacte + +No.2 ext. branch S.E. int. branch S.E. +Homo 1 1.28 0.65 16 5.37 1.32 +Xenopus 2 2.49 0.84 17 6.08 1.38 +Drosophil 3 4.10 1.12 18 2.05 0.96 +Artemia 4 8.63 1.57 19 3.25 1.07 +Saccharom 5 5.49 1.29 20 5.28 1.34 +Candida 6 3.88 1.12 21 5.37 1.40 +Mucor 7 4.97 1.20 22 18.00 2.41 +Absidia 8 2.78 0.95 23 lower limit +Arabidops 9 2.01 0.75 24 35.20 4.06 +Lycopersi 10 1.23 0.60 25 10.46 2.29 +Sulpholob 11 37.25 4.13 26 6.28 2.10 +Thermococ 12 20.39 2.96 27 10.04 2.45 +Thermopla 13 25.25 3.20 TBL : 280.52 iter: 6 +Methanoco 14 25.15 3.28 ln L: -5949.46 +- 199.28 +Halobacte 15 28.24 3.46 AIC : 11990.92 lower limit: 0.001 +#3 + :-1 Homo + :--16 + : :-2 Xenopus + :-18 + : : :--3 Drosophil + : :--17 + : :---4 Artemia + :--20 + : : :-9 Arabidops + : :------19 + : :-10 Lycopersi +:------------24 +: : :--5 Saccharom +: : :--21 +: : : :--6 Candida +: :-23 +: : :--7 Mucor +: :--22 +: :-8 Absidia +: +:------------11 Sulpholob +: +: :-------12 Thermococ +:----27 + : :---------13 Thermopla + :---26 + : :---------14 Methanoco + :----25 + :----------15 Halobacte + +No.3 ext. branch S.E. int. branch S.E. +Homo 1 1.24 0.63 16 5.56 1.34 +Xenopus 2 2.52 0.84 17 5.84 1.36 +Drosophil 3 4.11 1.12 18 1.54 0.89 +Artemia 4 8.64 1.57 19 17.51 2.37 +Saccharom 5 5.57 1.30 20 3.20 1.23 +Candida 6 3.81 1.11 21 3.22 1.07 +Mucor 7 5.08 1.21 22 5.23 1.33 +Absidia 8 2.67 0.92 23 2.86 1.17 +Arabidops 9 2.01 0.74 24 34.39 3.99 +Lycopersi 10 1.23 0.60 25 10.32 2.28 +Sulpholob 11 36.97 4.13 26 6.60 2.17 +Thermococ 12 20.34 2.97 27 9.94 2.43 +Thermopla 13 25.27 3.21 TBL : 279.10 iter: 6 +Methanoco 14 25.14 3.28 ln L: -5943.64 +- 199.09 +Halobacte 15 28.29 3.46 AIC : 11979.29 + +protml 2.3b3 JTT-F 3 trees 15 OTUs 409 sites. test15.ptn + +Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL +----------------------------------------------------------- +1 -5932.7 0.0 <-best 46 11957.4 0.0 ME +2 -5949.5 -16.7 7.8 46 11990.9 33.5 5.3 +3 -5943.6 -10.9 9.2 46 11979.3 21.9 3.9 --- molphy-2.3b3.orig/debian/tests/compare/test15.nj +++ molphy-2.3b3/debian/tests/compare/test15.nj @@ -0,0 +1,31 @@ +njdist 1.2.5 (11/09/01) 15 OTUs 409 sites JTT test15.ptn + + :-1 Homo + :--21 + : :-2 Xenopus + :-27 + : : :--3 Drosophil + : :--22 + : :---4 Artemia + :-26 + : : :--5 Saccharom + : : :-24 + : : : :--6 Candida + : :--25 + : : :--7 Mucor + : :--23 + : :-8 Absidia + :----------19 + : : :-9 Arabidops + : :-----20 + : :-10 Lycopersi + :-18 + : :------------11 Sulpholob + :-17 + : :--------12 Thermococ +:--16 +: :--------13 Thermopla +: +:--------14 Methanoco +: +:----------15 Halobacte --- molphy-2.3b3.orig/debian/tests/compare/test15.nj-2.2 +++ molphy-2.3b3/debian/tests/compare/test15.nj-2.2 @@ -0,0 +1,33 @@ +njdist 1.2.1 Jul 2 1994 15 OTUs 409 sites JTT test15.ptn + + :-1 Homo +:--21 +: :-2 Xenopus +: +: :--3 Drosophil +:--22 +: :---4 Artemia +: +: :--5 Saccharom +: :-24 +: : :--6 Candida +: :--25 +: : : :--7 Mucor +: : :--23 +: : :-8 Absidia +:-27 + : :-9 Arabidops + : :-----20 + : : :-10 Lycopersi + :-26 + : :------------11 Sulpholob + :----------19 + : :--------12 Thermococ + :-18 + : :--------13 Thermopla + :-17 + : :--------14 Methanoco + :--16 + :----------15 Halobacte + +((Homo,Xenopus),(Drosophil,Artemia),(((Saccharom,Candida),(Mucor,Absidia)),((Arabidops,Lycopersi),(Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte))))))); --- molphy-2.3b3.orig/debian/tests/compare/test15.njo +++ molphy-2.3b3/debian/tests/compare/test15.njo @@ -0,0 +1,31 @@ +njdist 1.2.5 (11/09/01) 15 OTUs 409 sites JTT test15.ptn + + :-1 Homo + :--21 + : :-2 Xenopus + :-27 + : : :--3 Drosophil + : :--22 + : :---4 Artemia + :-26 + : : :--5 Saccharom + : : :-24 + : : : :--6 Candida + : :--25 + : : :--7 Mucor + : :--23 + : :-8 Absidia +:----------19 +: : :-9 Arabidops +: :-----20 +: :-10 Lycopersi +: +:------------11 Sulpholob +: +: :--------12 Thermococ +:-18 + : :--------13 Thermopla + :-17 + : :--------14 Methanoco + :--16 + :----------15 Halobacte --- molphy-2.3b3.orig/debian/tests/compare/test15.tpl +++ molphy-2.3b3/debian/tests/compare/test15.tpl @@ -0,0 +1,29 @@ +3 / 3 protml 2.3b3 "JTT-F" 15 OTUs 409 sites. test15.ptn +# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL +# range TBL trees +# < 247.49 0 +# 5% 256.06 3 ************************************************** +# 10% 264.64 0 +# 15% 273.22 0 +# 20% 281.80 0 +# 25% 290.38 0 +# 30% 298.96 0 +# 35% 307.54 0 +# 40% 316.12 0 +# 45% 324.69 0 +# 50% 333.27 0 +# 55% 341.85 0 +# 60% 350.43 0 +# 65% 359.01 0 +# 70% 367.59 0 +# 75% 376.17 0 +# 80% 384.74 0 +# 85% 393.32 0 +# 90% 401.90 0 +# 95% 410.48 0 +# 100% 419.06 0 +# over 0 +# approx. ln L -5967.7 ... -5979.3 diff 11.5, TBL 247.5 ... 248.3 diff 0.8 +(((((Homo,Xenopus),(Drosophil,Artemia)),((Saccharom,Candida),(Mucor,Absidia))),(Arabidops,Lycopersi)),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 0.0 +((((Homo,Xenopus),(Drosophil,Artemia)),(((Saccharom,Candida),(Mucor,Absidia)),(Arabidops,Lycopersi))),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 10.7 +(((((Homo,Xenopus),(Drosophil,Artemia)),(Arabidops,Lycopersi)),((Saccharom,Candida),(Mucor,Absidia))),Sulpholob,(Thermococ,(Thermopla,(Methanoco,Halobacte)))); 11.5 --- molphy-2.3b3.orig/debian/tests/compare/test15.tree +++ molphy-2.3b3/debian/tests/compare/test15.tree @@ -0,0 +1,5 @@ +(((((Homo:1.456,Xenopus:2.215):5.159,(Drosophil:5.257,Artemia:7.247):3.724) +:1.075,((Saccharom:5.073,Candida:4.014):2.615,(Mucor:4.444,Absidia:2.810) +:3.308):3.309):1.947,(Arabidops:1.604,Lycopersi:1.554):12.729):26.645, +Sulpholob:33.726,(Thermococ:23.040,(Thermopla:23.538,(Methanoco:22.576, +Halobacte:28.715):4.132):1.271):2.403); --- molphy-2.3b3.orig/debian/tests/compare/test4.dis +++ molphy-2.3b3/debian/tests/compare/test4.dis @@ -0,0 +1,9 @@ +4 90 sites JTT test4.ptn +Data1 + 0.000000000000 0.253161436877 0.204206481653 0.228541838813 +Data2 + 0.253161436877 0.000000000000 0.167720557577 0.253821429711 +Data3 + 0.204206481653 0.167720557577 0.000000000000 0.218809727904 +Data4 + 0.228541838813 0.253821429711 0.218809727904 0.000000000000 --- molphy-2.3b3.orig/debian/tests/compare/test4.ml +++ molphy-2.3b3/debian/tests/compare/test4.ml @@ -0,0 +1,51 @@ +protml 2.3b3 (11/09/01) JTT 4 OTUs 90 sites. test4.ptn +#1 +:------------1 Data1 +: +: :------------2 Data2 +:--------5 +: :------3 Data3 +: +:------------4 Data4 + +No.1 ext. branch S.E. int. branch S.E. +Data1 1 11.72 4.07 5 6.01 3.04 +Data2 2 11.42 3.95 TBL : 46.07 iter: 5 +Data3 3 5.37 2.81 ln L: -461.51 +- 27.47 +Data4 4 11.55 4.14 AIC : 933.01 +#2 +:----------------1 Data1 +: +:-------------2 Data2 +: +: :-----------------4 Data4 +:--5 + :-------3 Data3 + +No.2 ext. branch S.E. int. branch S.E. +Data1 1 15.42 4.70 5 lower limit +Data2 2 12.07 4.15 TBL : 50.35 iter: 5 +Data3 3 6.63 3.18 ln L: -467.27 +- 27.92 +Data4 4 16.23 4.83 AIC : 944.55 lower limit: 0.001 +#3 + :----------------1 Data1 +:----5 +: :------3 Data3 +: +:-----------2 Data2 +: +:---------------4 Data4 + +No.3 ext. branch S.E. int. branch S.E. +Data1 1 15.11 4.60 5 2.77 2.25 +Data2 2 10.41 3.90 TBL : 48.85 iter: 6 +Data3 3 5.75 2.96 ln L: -465.53 +- 27.68 +Data4 4 14.80 4.61 AIC : 941.07 + +protml 2.3b3 JTT 3 trees 4 OTUs 90 sites. test4.ptn + +Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL RELL-BP +------------------------------------------------------------------- +1 -461.5 0.0 <-best 5 933.0 0.0 ME 0.7772 +2 -467.3 -5.8 4.3 5 944.5 11.5 4.3 0.0087 +3 -465.5 -4.0 5.3 5 941.1 8.1 2.8 0.2141 --- molphy-2.3b3.orig/debian/tests/compare/test4.nj +++ molphy-2.3b3/debian/tests/compare/test4.nj @@ -0,0 +1,9 @@ +njdist 1.2.5 (11/09/01) 4 OTUs 90 sites JTT test4.ptn + +:------------1 Data1 +: +: :-----------2 Data2 +:-----5 +: :-------3 Data3 +: +:------------4 Data4 --- molphy-2.3b3.orig/debian/tests/compare/test4.nj-2.2 +++ molphy-2.3b3/debian/tests/compare/test4.nj-2.2 @@ -0,0 +1,11 @@ +njdist 1.2.1 Jul 2 1994 4 OTUs 90 sites JTT test4.ptn + + :-----------1 Data1 +:-----5 +: :------------4 Data4 +: +:-----------2 Data2 +: +:-------3 Data3 + +((Data1,Data4),Data2,Data3); --- molphy-2.3b3.orig/debian/tests/compare/test4.tpl +++ molphy-2.3b3/debian/tests/compare/test4.tpl @@ -0,0 +1,29 @@ +3 / 3 protml 2.3b3 "JTT" 4 OTUs 90 sites. test4.ptn +# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL +# range TBL trees +# < 43.06 0 +# 5% 43.16 1 ************************************************** +# 10% 43.25 0 +# 15% 43.35 0 +# 20% 43.44 0 +# 25% 43.54 0 +# 30% 43.63 0 +# 35% 43.73 0 +# 40% 43.82 0 +# 45% 43.91 0 +# 50% 44.01 0 +# 55% 44.10 0 +# 60% 44.20 0 +# 65% 44.29 0 +# 70% 44.39 0 +# 75% 44.48 0 +# 80% 44.58 0 +# 85% 44.67 1 ************************************************** +# 90% 44.77 0 +# 95% 44.86 0 +# 100% 44.96 1 ************************************************** +# over 0 +# approx. ln L -462.1 ... -467.7 diff 5.6, TBL 43.1 ... 44.6 diff 1.5 +(Data1,(Data2,Data3),Data4); 0.0 +(Data1,Data2,(Data4,Data3)); 5.6 +((Data1,Data3),Data2,Data4); 5.6 --- molphy-2.3b3.orig/debian/tests/compare/test5.ml +++ molphy-2.3b3/debian/tests/compare/test5.ml @@ -0,0 +1,276 @@ +protml 2.3b3 (11/09/01) JTT 5 OTUs 352 sites. test5.ptn +#1 +:----------1 Tabac_chl +: +:------4 Fremyella +: +: :-----------------5 Synechocy +:---7 + : :-------2 Prochloro + :----6 + :--3 Anacystis + +No.1 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.38 1.76 6 2.28 0.92 +Prochloro 2 6.25 1.41 7 1.14 0.69 +Anacystis 3 1.50 0.74 TBL : 42.19 iter: 5 +Fremyella 4 5.43 1.34 ln L: -1793.14 +- 65.40 +Synechocy 5 16.21 2.36 AIC : 3600.27 +#2 + :----------1 Tabac_chl +:--7 +: : :-------2 Prochloro +: :----6 +: :--3 Anacystis +: +:------4 Fremyella +: +:----------------5 Synechocy + +No.2 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.78 1.80 6 2.57 0.99 +Prochloro 2 6.36 1.42 7 0.97 0.73 +Anacystis 3 1.43 0.74 TBL : 42.43 iter: 5 +Fremyella 4 5.34 1.36 ln L: -1796.92 +- 66.12 +Synechocy 5 15.98 2.36 AIC : 3607.84 +#3 +:----------1 Tabac_chl +: +: :-------4 Fremyella +:--7 +: : :-------2 Prochloro +: :----6 +: :--3 Anacystis +: +:-----------------5 Synechocy + +No.3 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.28 1.79 6 2.63 1.01 +Prochloro 2 6.35 1.42 7 0.91 0.80 +Anacystis 3 1.44 0.74 TBL : 42.74 iter: 6 +Fremyella 4 6.02 1.42 ln L: -1797.75 +- 65.83 +Synechocy 5 16.10 2.38 AIC : 3609.51 +#4 +:----------1 Tabac_chl +: +:------4 Fremyella +: +: :-------------------5 Synechocy +: :--6 +: : :--3 Anacystis +:----7 + :-------2 Prochloro + +No.4 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.46 1.75 6 lower limit +Prochloro 2 6.43 1.45 7 2.74 1.04 +Anacystis 3 1.89 0.86 TBL : 44.09 iter: 6 +Fremyella 4 5.50 1.35 ln L: -1804.43 +- 65.88 +Synechocy 5 18.08 2.49 AIC : 3622.87 lower limit: 0.001 +#5 +:----------1 Tabac_chl +: +:------4 Fremyella +: +: :------------------5 Synechocy +: :---6 +: : :------2 Prochloro +:----7 + :--3 Anacystis + +No.5 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.36 1.74 6 1.25 0.75 +Prochloro 2 5.31 1.35 7 2.74 1.03 +Anacystis 3 1.66 0.81 TBL : 43.00 iter: 6 +Fremyella 4 5.52 1.35 ln L: -1799.81 +- 65.48 +Synechocy 5 17.15 2.43 AIC : 3613.63 +#6 + :------------1 Tabac_chl + :--6 + : :--3 Anacystis +:----7 +: :-------2 Prochloro +: +:------4 Fremyella +: +:----------------5 Synechocy + +No.6 ext. branch S.E. int. branch S.E. +Tabac_chl 1 11.31 1.94 6 0.57 0.54 +Prochloro 2 6.10 1.44 7 2.61 1.09 +Anacystis 3 1.92 0.87 TBL : 43.48 iter: 6 +Fremyella 4 5.32 1.36 ln L: -1808.97 +- 66.86 +Synechocy 5 15.65 2.33 AIC : 3631.94 +#7 + :-----------1 Tabac_chl + :---6 + : :------2 Prochloro +:----7 +: :--3 Anacystis +: +:------4 Fremyella +: +:----------------5 Synechocy + +No.7 ext. branch S.E. int. branch S.E. +Tabac_chl 1 10.46 1.87 6 1.42 0.75 +Prochloro 2 5.22 1.36 7 2.70 1.10 +Anacystis 3 1.90 0.86 TBL : 42.94 iter: 6 +Fremyella 4 5.47 1.38 ln L: -1803.71 +- 66.47 +Synechocy 5 15.76 2.34 AIC : 3621.43 +#8 + :----------1 Tabac_chl +:---6 +: :-------2 Prochloro +: +:-------4 Fremyella +: +: :------------------5 Synechocy +:--7 + :---3 Anacystis + +No.8 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.72 1.79 6 1.41 0.75 +Prochloro 2 6.10 1.46 7 lower limit +Anacystis 3 2.88 1.01 TBL : 44.17 iter: 5 +Fremyella 4 6.95 1.51 ln L: -1810.28 +- 66.73 +Synechocy 5 17.11 2.42 AIC : 3634.55 lower limit: 0.001 +#9 +:----------1 Tabac_chl +: +: :--------4 Fremyella +: :--6 +: : :-------2 Prochloro +:----7 +: :---3 Anacystis +: +:-----------------5 Synechocy + +No.9 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.23 1.79 6 0.56 0.55 +Prochloro 2 6.48 1.48 7 2.31 1.09 +Anacystis 3 2.19 0.93 TBL : 44.01 iter: 7 +Fremyella 4 7.22 1.56 ln L: -1811.22 +- 66.41 +Synechocy 5 16.01 2.36 AIC : 3636.44 +#10 + :-----------1 Tabac_chl +:--6 +: :---3 Anacystis +: +:-------4 Fremyella +: +: :-----------------5 Synechocy +:---7 + :-------2 Prochloro + +No.10 ext. branch S.E. int. branch S.E. +Tabac_chl 1 10.42 1.84 6 0.40 0.50 +Prochloro 2 6.13 1.45 7 1.22 0.75 +Anacystis 3 2.75 0.98 TBL : 43.67 iter: 5 +Fremyella 4 6.67 1.48 ln L: -1810.93 +- 66.72 +Synechocy 5 16.08 2.35 AIC : 3635.87 +#11 + :----------1 Tabac_chl +:---6 +: :-------2 Prochloro +: +: :-------4 Fremyella +:--7 +: :---3 Anacystis +: +:------------------5 Synechocy + +No.11 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.72 1.79 6 1.41 0.75 +Prochloro 2 6.10 1.46 7 lower limit +Anacystis 3 2.88 1.01 TBL : 44.17 iter: 5 +Fremyella 4 6.95 1.51 ln L: -1810.28 +- 66.73 +Synechocy 5 17.11 2.42 AIC : 3634.56 lower limit: 0.001 +#12 + :-----------1 Tabac_chl +:--6 +: :---3 Anacystis +: +: :-------4 Fremyella +:--7 +: :--------2 Prochloro +: +:-----------------5 Synechocy + +No.12 ext. branch S.E. int. branch S.E. +Tabac_chl 1 10.56 1.85 6 0.31 0.46 +Prochloro 2 7.03 1.52 7 0.43 0.50 +Anacystis 3 2.74 0.97 TBL : 44.63 iter: 6 +Fremyella 4 6.59 1.48 ln L: -1814.74 +- 67.02 +Synechocy 5 16.97 2.42 AIC : 3643.48 +#13 +:-----------1 Tabac_chl +: +: :-------4 Fremyella +:--6 +: :---3 Anacystis +: +: :-----------------5 Synechocy +:---7 + :-------2 Prochloro + +No.13 ext. branch S.E. int. branch S.E. +Tabac_chl 1 10.44 1.84 6 0.02 0.45 +Prochloro 2 6.24 1.46 7 1.39 0.78 +Anacystis 3 2.83 0.99 TBL : 43.86 iter: 7 +Fremyella 4 6.85 1.49 ln L: -1811.42 +- 66.77 +Synechocy 5 16.09 2.35 AIC : 3636.84 +#14 +:-----------1 Tabac_chl +: +: :-------4 Fremyella +:--6 +: :--------2 Prochloro +: +: :------------------5 Synechocy +:--7 + :---3 Anacystis + +No.14 ext. branch S.E. int. branch S.E. +Tabac_chl 1 10.62 1.86 6 0.56 0.54 +Prochloro 2 7.14 1.53 7 lower limit +Anacystis 3 2.84 0.99 TBL : 44.87 iter: 5 +Fremyella 4 6.56 1.47 ln L: -1815.13 +- 67.02 +Synechocy 5 17.15 2.43 AIC : 3644.26 lower limit: 0.001 +#15 +:----------1 Tabac_chl +: +: :--------4 Fremyella +: :--6 +: : :---3 Anacystis +:----7 +: :-------2 Prochloro +: +:-----------------5 Synechocy + +No.15 ext. branch S.E. int. branch S.E. +Tabac_chl 1 9.20 1.79 6 0.09 0.50 +Prochloro 2 6.74 1.51 7 2.34 1.10 +Anacystis 3 2.32 0.95 TBL : 44.27 iter: 7 +Fremyella 4 7.57 1.59 ln L: -1812.58 +- 66.59 +Synechocy 5 16.01 2.36 AIC : 3639.16 + +protml 2.3b3 JTT 15 trees 5 OTUs 352 sites. test5.ptn + +Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL +----------------------------------------------------------- +1 -1793.1 0.0 <-best 7 3600.3 0.0 ME +2 -1796.9 -3.8 6.0 7 3607.8 7.6 0.2 +3 -1797.8 -4.6 5.6 7 3609.5 9.2 0.5 +4 -1804.4 -11.3 6.4 7 3622.9 22.6 1.9 +5 -1799.8 -6.7 8.1 7 3613.6 13.4 0.8 +6 -1809.0 -15.8 10.0 7 3631.9 31.7 1.3 +7 -1803.7 -10.6 11.4 7 3621.4 21.2 0.7 +8 -1810.3 -17.1 11.8 7 3634.6 34.3 2.0 +9 -1811.2 -18.1 10.3 7 3636.4 36.2 1.8 +10 -1810.9 -17.8 11.5 7 3635.9 35.6 1.5 +11 -1810.3 -17.1 11.8 7 3634.6 34.3 2.0 +12 -1814.7 -21.6 10.7 7 3643.5 43.2 2.4 +13 -1811.4 -18.3 11.4 7 3636.8 36.6 1.7 +14 -1815.1 -22.0 10.6 7 3644.3 44.0 2.7 +15 -1812.6 -19.4 9.8 7 3639.2 38.9 2.1 --- molphy-2.3b3.orig/debian/tests/compare/test5.nj +++ molphy-2.3b3/debian/tests/compare/test5.nj @@ -0,0 +1,18 @@ +njdist 1.2.5 (11/09/01) 5 OTUs 352 sites JTT test5.ptn + + :---------1 Tabac_chl +:--7 +: : :------2 Prochloro +: :---6 +: :---3 Anacystis +: +:------4 Fremyella +: +:---------------5 Synechocy + + num length num length +Tabac_chl 1 8.91 6 1.24 +Prochloro 2 5.17 7 0.63 +Anacystis 3 2.55 +Fremyella 4 5.41 +Synechocy 5 14.94 --- molphy-2.3b3.orig/debian/tests/compare/test5.tpl +++ molphy-2.3b3/debian/tests/compare/test5.tpl @@ -0,0 +1,41 @@ +15 / 15 protml 2.3b3 "JTT" 5 OTUs 352 sites. test5.ptn +# <= 105 trees (top ranking for approx. ln L) in the top 200.0% range of TBL +# range TBL trees +# < 38.85 0 +# 5% 38.94 1 ************ +# 10% 39.03 0 +# 15% 39.12 1 ************ +# 20% 39.21 0 +# 25% 39.30 1 ************ +# 30% 39.39 0 +# 35% 39.48 1 ************ +# 40% 39.57 1 ************ +# 45% 39.66 1 ************ +# 50% 39.75 0 +# 55% 39.84 0 +# 60% 39.93 4 ************************************************** +# 65% 40.02 1 ************ +# 70% 40.11 0 +# 75% 40.20 1 ************ +# 80% 40.29 0 +# 85% 40.38 1 ************ +# 90% 40.47 1 ************ +# 95% 40.56 0 +# 100% 40.65 1 ************ +# over 0 +# approx. ln L -1798.8 ... -1818.0 diff 19.1, TBL 39.0 ... 39.9 diff 0.9 +(Tabac_chl,Fremyella,(Synechocy,(Prochloro,Anacystis))); 0.0 +((Tabac_chl,(Prochloro,Anacystis)),Fremyella,Synechocy); 0.9 +(Tabac_chl,(Fremyella,(Prochloro,Anacystis)),Synechocy); 1.9 +(Tabac_chl,Fremyella,((Synechocy,Anacystis),Prochloro)); 9.3 +(Tabac_chl,Fremyella,((Synechocy,Prochloro),Anacystis)); 10.2 +(((Tabac_chl,Anacystis),Prochloro),Fremyella,Synechocy); 13.6 +(((Tabac_chl,Prochloro),Anacystis),Fremyella,Synechocy); 13.6 +((Tabac_chl,Prochloro),Fremyella,(Synechocy,Anacystis)); 14.4 +(Tabac_chl,((Fremyella,Prochloro),Anacystis),Synechocy); 16.7 +((Tabac_chl,Anacystis),Fremyella,(Synechocy,Prochloro)); 16.7 +((Tabac_chl,Prochloro),(Fremyella,Anacystis),Synechocy); 17.6 +((Tabac_chl,Anacystis),(Fremyella,Prochloro),Synechocy); 17.9 +(Tabac_chl,(Fremyella,Anacystis),(Synechocy,Prochloro)); 18.0 +(Tabac_chl,(Fremyella,Prochloro),(Synechocy,Anacystis)); 18.5 +(Tabac_chl,((Fremyella,Anacystis),Prochloro),Synechocy); 19.1 --- molphy-2.3b3.orig/debian/tests/compare/test6.ml +++ molphy-2.3b3/debian/tests/compare/test6.ml @@ -0,0 +1,216 @@ +nucml 2.3b3 (11/09/01) A/B:30.58 F 6 OTUs 1344 sites. test6.nuc +#1 + :--1 Chimp + :---7 + : :-2 Bonobo + :---8 + : :-----3 Human +:-----9 +: :-----4 Gorilla +: +:----------5 Orang +: +:----------------6 Siamang + +No.1 ext. branch S.E. int. branch S.E. +Chimp 1 6.55 0.93 7 9.54 1.76 +Bonobo 2 4.06 0.83 8 9.50 2.21 +Human 3 20.07 2.12 9 16.61 3.96 +Gorilla 4 20.98 2.60 TBL : 213.70 iter: 7 +Orang 5 47.78 5.82 ln L: -5539.83 +- 79.93 +Siamang 6 78.61 8.58 AIC : 11105.67 +#2 + :--1 Chimp + :---7 + : :-2 Bonobo +:---8 +: :-----3 Human +: +: :-------------5 Orang +:--9 +: :-----4 Gorilla +: +:--------------------6 Siamang + +No.2 ext. branch S.E. int. branch S.E. +Chimp 1 6.57 0.94 7 9.47 1.76 +Bonobo 2 4.04 0.83 8 8.98 2.17 +Human 3 20.11 2.12 9 1.75 1.58 +Gorilla 4 20.05 2.59 TBL : 230.46 iter: 8 +Orang 5 63.98 6.32 ln L: -5555.52 +- 80.45 +Siamang 6 95.51 9.43 AIC : 11137.04 +#3 + :--1 Chimp + :----7 + : :-2 Bonobo +:------9 +: : :-----3 Human +: :--8 +: :------4 Gorilla +: +:----------5 Orang +: +:----------------6 Siamang + +No.3 ext. branch S.E. int. branch S.E. +Chimp 1 6.58 0.94 7 10.37 1.81 +Bonobo 2 4.02 0.83 8 lower limit +Human 3 20.17 2.15 9 23.47 4.64 +Gorilla 4 29.43 2.77 TBL : 219.77 iter: 7 +Orang 5 47.88 6.03 ln L: -5559.12 +- 81.31 +Siamang 6 77.86 8.64 AIC : 11144.23 lower limit: 0.001 +#4 + :--1 Chimp + :----7 + : :-2 Bonobo + :--8 + : :------4 Gorilla +:------9 +: :-----3 Human +: +:----------5 Orang +: +:----------------6 Siamang + +No.4 ext. branch S.E. int. branch S.E. +Chimp 1 6.58 0.94 7 10.37 1.81 +Bonobo 2 4.02 0.83 8 lower limit +Human 3 20.17 2.15 9 23.47 4.64 +Gorilla 4 29.43 2.77 TBL : 219.77 iter: 7 +Orang 5 47.88 6.03 ln L: -5559.12 +- 81.31 +Siamang 6 77.86 8.64 AIC : 11144.23 lower limit: 0.001 +#5 + :--1 Chimp + :---7 + : :-2 Bonobo +:---8 +: :-----3 Human +: +:-------------5 Orang +: +: :--------------------6 Siamang +:--9 + :-----4 Gorilla + +No.5 ext. branch S.E. int. branch S.E. +Chimp 1 6.56 0.93 7 9.52 1.76 +Bonobo 2 4.05 0.83 8 9.82 2.23 +Human 3 20.07 2.12 9 lower limit +Gorilla 4 20.94 2.61 TBL : 231.52 iter: 7 +Orang 5 64.53 6.39 ln L: -5556.18 +- 80.47 +Siamang 6 96.03 9.48 AIC : 11138.37 lower limit: 0.001 +#6 + :--1 Chimp +:---7 +: :-2 Bonobo +: +: :-------------5 Orang +: :---8 +: : :-----4 Gorilla +:--9 +: :-----3 Human +: +:---------------------6 Siamang + +No.6 ext. branch S.E. int. branch S.E. +Chimp 1 6.63 0.94 7 8.46 1.78 +Bonobo 2 3.97 0.83 8 9.88 2.29 +Human 3 20.10 2.14 9 1.52 1.52 +Gorilla 4 20.18 2.58 TBL : 239.04 iter: 14 +Orang 5 64.30 6.35 ln L: -5571.97 +- 81.57 +Siamang 6 103.99 10.17 AIC : 11169.93 +#7 + :--1 Chimp +:---7 +: :-2 Bonobo +: +: :-------------5 Orang +:---8 +: :-----4 Gorilla +: +: :---------------------6 Siamang +:--9 + :-----3 Human + +No.7 ext. branch S.E. int. branch S.E. +Chimp 1 6.61 0.94 7 9.90 1.80 +Bonobo 2 4.00 0.83 8 9.85 2.29 +Human 3 20.22 2.15 9 lower limit +Gorilla 4 20.20 2.58 TBL : 239.75 iter: 9 +Orang 5 64.34 6.35 ln L: -5572.27 +- 81.55 +Siamang 6 104.63 10.20 AIC : 11170.54 lower limit: 0.001 +#8 + :--1 Chimp +:----7 +: :-2 Bonobo +: +: :---------------5 Orang +:--9 +: : :-----3 Human +: :--8 +: :------4 Gorilla +: +:---------------------6 Siamang + +No.8 ext. branch S.E. int. branch S.E. +Chimp 1 6.63 0.94 7 10.72 1.88 +Bonobo 2 3.95 0.83 8 lower limit +Human 3 20.53 2.21 9 0.64 1.29 +Gorilla 4 28.35 2.71 TBL : 241.75 iter: 9 +Orang 5 70.17 6.83 ln L: -5584.22 +- 82.66 +Siamang 6 100.76 9.87 AIC : 11194.43 lower limit: 0.001 +#9 + :--1 Chimp +:----7 +: :-2 Bonobo +: +: :---------------5 Orang +:--8 +: :----3 Human +: +: :--------------------6 Siamang +:---9 + :-----4 Gorilla + +No.9 ext. branch S.E. int. branch S.E. +Chimp 1 6.58 0.94 7 10.33 1.82 +Bonobo 2 4.01 0.83 8 1.60 1.67 +Human 3 18.65 2.15 9 6.94 2.23 +Gorilla 4 22.47 2.66 TBL : 238.62 iter: 12 +Orang 5 71.52 7.02 ln L: -5579.67 +- 82.13 +Siamang 6 96.51 9.54 AIC : 11185.34 +#10 + :--1 Chimp +:----7 +: :-2 Bonobo +: +: :--------------5 Orang +: :--8 +: : :----3 Human +:--9 +: :------4 Gorilla +: +:---------------------6 Siamang + +No.10 ext. branch S.E. int. branch S.E. +Chimp 1 6.64 0.94 7 10.64 1.87 +Bonobo 2 3.94 0.83 8 1.05 1.50 +Human 3 19.55 2.20 9 0.60 1.28 +Gorilla 4 28.39 2.72 TBL : 241.38 iter: 9 +Orang 5 69.75 6.82 ln L: -5584.00 +- 82.68 +Siamang 6 100.81 9.88 AIC : 11194.01 + +nucml 2.3b3 A/B:30.58 F 10 trees 6 OTUs 1344 sites. test6.nuc + +Tree ln L Diff ln L S.E. #Para AIC Diff AIC TBL +----------------------------------------------------------- +1 -5539.8 0.0 <-best 13 11105.7 0.0 ME +2 -5555.5 -15.7 7.0 13 11137.0 31.4 16.8 +3 -5559.1 -19.3 8.2 13 11144.2 38.6 6.1 +4 -5559.1 -19.3 8.2 13 11144.2 38.6 6.1 +5 -5556.2 -16.3 6.8 13 11138.4 32.7 17.8 +6 -5572.0 -32.1 10.7 13 11169.9 64.3 25.3 +7 -5572.3 -32.4 10.5 13 11170.5 64.9 26.0 +8 -5584.2 -44.4 13.1 13 11194.4 88.8 28.1 +9 -5579.7 -39.8 11.2 13 11185.3 79.7 24.9 +10 -5584.0 -44.2 13.2 13 11194.0 88.3 27.7 --- molphy-2.3b3.orig/debian/tests/compare/test6.mlq +++ molphy-2.3b3/debian/tests/compare/test6.mlq @@ -0,0 +1,22 @@ +nucml 2.3b3 (11/09/01) A/B:opt F 6 OTUs 1344 sites. test6.nuc +#1 +Alpha/Beta: 30.987 + :----1 Chimp + :------7 + : :--2 Bonobo + :------8 + : :----------3 Human +:---------9 +: :----------4 Gorilla +: +:-----------------------5 Orang +: +:--------------------------------------6 Siamang + +No.1 ext. branch S.E. int. branch S.E. +Chimp 1 6.56 0.94 7 9.55 1.76 +Bonobo 2 4.06 0.83 8 9.53 2.22 +Human 3 20.09 2.13 9 16.70 3.99 +Gorilla 4 21.01 2.61 TBL : 214.99 iter: 9 +Orang 5 48.11 5.88 ln L: -5539.83 +- 79.97 +Siamang 6 79.39 8.71 AIC : 11105.65 --- molphy-2.3b3.orig/debian/tests/compare/test6.mls +++ molphy-2.3b3/debian/tests/compare/test6.mls @@ -0,0 +1,45 @@ +nucml 2.3b3 (11/09/01) A/B:4.00 F 6 OTUs 1344 sites. test6.nuc +#0 +:----1 Chimp +: +:---2 Bonobo +: +:-----------3 Human +: +:-------------4 Gorilla +: +:--------------------5 Orang +: +:------------------------6 Siamang +#1 + :---1 Chimp +:------7 +: :--2 Bonobo +: +:--------3 Human +: +:----------4 Gorilla +: +: :------------5 Orang +:--------8 + :-----------------6 Siamang + + :---1 Chimp + :-----7 + : :--2 Bonobo + :----9 + : :--------3 Human +:-------8 +: :--------4 Gorilla +: +:------------5 Orang +: +:-----------------6 Siamang + +No.1 ext. branch S.E. int. branch S.E. +Chimp 1 6.01 0.81 7 8.31 1.19 +Bonobo 2 3.95 0.71 8 11.59 1.82 +Human 3 16.01 1.46 9 6.04 1.29 +Gorilla 4 17.01 1.61 TBL : 128.72 iter: 7 +Orang 5 24.67 2.18 ln L: -5889.71 +- 80.88 +Siamang 6 35.12 2.57 AIC : 11805.42 --- molphy-2.3b3.orig/debian/tests/compare/test6.mls-2.2 +++ molphy-2.3b3/debian/tests/compare/test6.mls-2.2 @@ -0,0 +1,25 @@ +nucml 2.2 Jul 2 1994 A/B:4.00 F 6 OTUs 1344 sites test6.nuc + +((Chimp,Bonobo),Human,Gorilla,Orang,Siamang); +((Chimp,Bonobo),Human,Gorilla,(Orang,Siamang)); +(((Chimp,Bonobo),Human),Gorilla,(Orang,Siamang)); + + :---1 Chimp + :-----7 + : :--2 Bonobo +:----9 +: :--------3 Human +: +:--------4 Gorilla +: +: :------------5 Orang +:-------8 + :-----------------6 Siamang + +No.1 num length S.E. num length S.E. +Chimp 1 5.96 0.80 7 8.23 1.18 +Bonobo 2 3.91 0.70 8 11.49 1.81 +Human 3 15.88 1.45 9 6.00 1.28 +Gorilla 4 16.87 1.60 6 +Orang 5 24.48 2.17 ln L: -5886.55 +- 80.83 +Siamang 6 34.86 2.55 AIC : 11799.10 --- molphy-2.3b3.orig/debian/tests/compare/test6.tpl +++ molphy-2.3b3/debian/tests/compare/test6.tpl @@ -0,0 +1,36 @@ +10 / 105 nucml 2.3b3 "A/B:30.58 F" 6 OTUs 1344 sites. test6.nuc +# <= 10 trees (top ranking for approx. ln L) in the top 200.0% range of TBL +# range TBL trees +# < 216.29 0 +# 5% 217.80 1 *** +# 10% 219.31 2 ******* +# 15% 220.82 0 +# 20% 222.33 2 ******* +# 25% 223.84 1 *** +# 30% 225.35 3 ********** +# 35% 226.86 7 ************************* +# 40% 228.37 7 ************************* +# 45% 229.88 5 ***************** +# 50% 231.39 1 *** +# 55% 232.90 3 ********** +# 60% 234.41 4 ************** +# 65% 235.92 7 ************************* +# 70% 237.43 14 ************************************************** +# 75% 238.94 11 *************************************** +# 80% 240.45 11 *************************************** +# 85% 241.96 10 *********************************** +# 90% 243.47 8 **************************** +# 95% 244.98 5 ***************** +# 100% 246.49 3 ********** +# over 0 +# approx. ln L -5542.7 ... -5589.1 diff 46.5, TBL 216.3 ... 228.5 diff 12.3 +((((Chimp,Bonobo),Human),Gorilla),Orang,Siamang); 0.0 +(((Chimp,Bonobo),Human),(Orang,Gorilla),Siamang); 17.2 +(((Chimp,Bonobo),(Human,Gorilla)),Orang,Siamang); 18.9 +((((Chimp,Bonobo),Gorilla),Human),Orang,Siamang); 19.1 +(((Chimp,Bonobo),Human),Orang,(Siamang,Gorilla)); 20.6 +((Chimp,Bonobo),((Orang,Gorilla),Human),Siamang); 41.2 +((Chimp,Bonobo),(Orang,Gorilla),(Siamang,Human)); 44.2 +((Chimp,Bonobo),(Orang,(Human,Gorilla)),Siamang); 46.2 +((Chimp,Bonobo),(Orang,Human),(Siamang,Gorilla)); 46.4 +((Chimp,Bonobo),((Orang,Human),Gorilla),Siamang); 46.5 --- molphy-2.3b3.orig/debian/tests/compare/test6.tplq +++ molphy-2.3b3/debian/tests/compare/test6.tplq @@ -0,0 +1,2 @@ +1 / 3 A/B:4.00 F model approx ln L -5903.3 ... -5903.3 diff 0.0 +((((Chimp,Bonobo),Human),Gorilla),Orang,Siamang); --- molphy-2.3b3.orig/debian/tests/compare/test7.mlq +++ molphy-2.3b3/debian/tests/compare/test7.mlq @@ -0,0 +1,24 @@ +protml 2.3b3 (11/09/01) JTT-F 7 OTUs 409 sites. test7.ptn +#1 + :--1 Homo + :--8 + : :----2 Drosophil +:---10 +: : :---3 Saccharom +: :---9 +: :----4 Mucor +: +: :-5 Arabidops +:----11 +: :-6 Lycopersi +: +:-----------------------7 Sulpholob + +No.1 ext. branch S.E. int. branch S.E. +Homo 1 5.69 1.32 8 2.54 1.00 +Drosophil 2 9.80 1.70 9 4.44 1.27 +Saccharom 3 8.31 1.60 10 6.06 1.71 +Mucor 4 9.17 1.65 11 10.81 2.04 +Arabidops 5 2.05 0.76 TBL : 126.70 iter: 6 +Lycopersi 6 1.18 0.60 ln L: -3155.25 +- 98.78 +Sulpholob 7 66.64 5.52 AIC : 6370.50 --- molphy-2.3b3.orig/debian/tests/compare/test7.mls +++ molphy-2.3b3/debian/tests/compare/test7.mls @@ -0,0 +1,52 @@ +protml 2.3b3 (11/09/01) JTT-F 7 OTUs 409 sites. test7.ptn +#0 +:----1 Homo +: +:-----2 Drosophil +: +:-----3 Saccharom +: +:-----4 Mucor +: +:------5 Arabidops +: +:------6 Lycopersi +: +:-------------------------7 Sulpholob +#1 + :--1 Homo +:-10 +: :----2 Drosophil +: +: :---3 Saccharom +:---9 +: :----4 Mucor +: +: :-5 Arabidops +:-------8 +: :-6 Lycopersi +: +:-------------------------7 Sulpholob + + :--1 Homo + :-10 + : :----2 Drosophil +:---11 +: : :---3 Saccharom +: :---9 +: :----4 Mucor +: +: :-5 Arabidops +:-----8 +: :-6 Lycopersi +: +:-----------------------7 Sulpholob + +No.1 ext. branch S.E. int. branch S.E. +Homo 1 5.69 1.32 8 10.81 2.04 +Drosophil 2 9.80 1.70 9 4.44 1.27 +Saccharom 3 8.31 1.60 10 2.54 1.00 +Mucor 4 9.17 1.65 11 6.06 1.71 +Arabidops 5 2.05 0.76 TBL : 126.70 iter: 6 +Lycopersi 6 1.18 0.60 ln L: -3155.25 +- 98.78 +Sulpholob 7 66.64 5.52 AIC : 6370.50 --- molphy-2.3b3.orig/debian/tests/compare/test7.mls-2.2 +++ molphy-2.3b3/debian/tests/compare/test7.mls-2.2 @@ -0,0 +1,29 @@ +protml 2.2 Jul 2 1994 JTT-F 7 OTUs 409 sites test7.ptn + +(Homo,Drosophil,Saccharom,Mucor,(Arabidops,Lycopersi),Sulpholob); +(Homo,Drosophil,(Saccharom,Mucor),(Arabidops,Lycopersi),Sulpholob); +(Homo,Drosophil,(Saccharom,Mucor),((Arabidops,Lycopersi),Sulpholob)); +(Homo,Drosophil,((Saccharom,Mucor),((Arabidops,Lycopersi),Sulpholob))); + +:--1 Homo +: +:----2 Drosophil +: +: :---3 Saccharom +: :---9 +: : :----4 Mucor +:-11 + : :-5 Arabidops + : :-----8 + : : :-6 Lycopersi + :---10 + :-----------------------7 Sulpholob + +No.1 num length S.E. num length S.E. +Homo 1 5.65 1.31 8 10.74 2.03 +Drosophil 2 9.73 1.69 9 4.42 1.27 +Saccharom 3 8.26 1.59 10 6.03 1.70 +Mucor 4 9.11 1.64 11 2.53 0.99 +Arabidops 5 2.04 0.75 8 +Lycopersi 6 1.18 0.60 ln L: -3155.53 +- 98.80 +Sulpholob 7 66.34 5.49 AIC : 6371.06 --- molphy-2.3b3.orig/debian/tests/compare/test7.tpl +++ molphy-2.3b3/debian/tests/compare/test7.tpl @@ -0,0 +1,2 @@ +1 / 3 JTT-F model approx ln L -3162.6 ... -3162.6 diff 0.0 +(((Homo,Drosophil),(Saccharom,Mucor)),(Arabidops,Lycopersi),Sulpholob); --- molphy-2.3b3.orig/debian/tests/comparetests +++ molphy-2.3b3/debian/tests/comparetests @@ -0,0 +1,47 @@ +#!/bin/sh +# This script is a helper script for testing the molphy components +# It was written for the Debian GNU/Linux distribution by +# Andreas Tille + +echo Testing $1 ... +COMPARE=/usr/share/doc/molphy/examples/tests/compare + +if [ _$1 = _ ] ; then + echo Usage: $0 "" + exit -1 +fi + +if [ ! -d $COMPARE ] ; then + echo Broken installation. + echo Directory $COMPARE with test results is missing. + exit -1 +fi + +if [ ! -f $1 ] ; then + echo $1 not found. + exit -1 +fi + +if [ ! -f ${COMPARE}/$1 -a ! -f ${COMPARE}/$1.gz ] ; then + echo Broken installation. + echo File ${COMPARE}/$1 with test results is missing. + exit -1 +fi + +## The first line contains the date the test was done so we have +## to delete it for comparison ... + +if [ -f ${COMPARE}/$1 ] ; then + sed "1d" ${COMPARE}/$1 > $1.comp +else + zcat ${COMPARE}/$1 | sed "1d" > $1.comp +fi + +sed "1d" $1 > $1.test + +diff $1.comp $1.test + +if [ -f ${COMPARE}/$1-2.2 ] ; then + echo Note: There where explictite differences to molphy version 2.2 + echo Please read ${COMPARE}/README.compare +fi --- molphy-2.3b3.orig/debian/tests/makefile +++ molphy-2.3b3/debian/tests/makefile @@ -0,0 +1,70 @@ +#!/usr/bin/make + +# This makefile was written to test the output of the molphy components +# It was written for the Debian GNU/Linux distribution by +# Andreas Tille + +all: comparetests protml nucml njdist + @echo All tests successfully done! + +protml: test4.ptn test5.ptn test15.ptn test15.cns + protml -e test4.ptn > test4.tpl + @comparetests test4.tpl + protml test4.ptn test4.tpl > test4.ml + @comparetests test4.ml + protml -e test5.ptn | tee test5.tpl | protml -b test5.ptn - > test5.ml + @comparetests test5.tpl + @comparetests test5.ml + protml -ef test15.ptn test15.cns > test15.tpl + @comparetests test15.tpl + protml -fb test15.ptn test15.tpl > test15.ml + @comparetests test15.ml + protml -sf test7.ptn > test7.mls + @comparetests test7.mls + protml -qf -n3 test7.ptn > test7.tpl + @comparetests test7.tpl + protml -fb test7.ptn test7.tpl > test7.mlq + @comparetests test7.mlq + @echo All $@ successfully done! + +nucml: test6.nuc + nucml -s test6.nuc > test6.mls + @comparetests test6.mls + nucml -q -n3 test6.nuc > test6.tplq + @comparetests test6.tplq + nucml -b -topt test6.nuc test6.tplq > test6.mlq + @comparetests test6.mlq + nucml -e -t30.58 -n10 test6.nuc > test6.tpl + @comparetests test6.tpl + nucml -b -t30.58 test6.nuc test6.tpl > test6.ml + @comparetests test6.ml + @echo All $@ successfully done! + +njdist: test4.ptn test15.tree + protml -D test4.ptn > test4.dis + @comparetests test4.dis + njdist test4.dis > test4.nj + @comparetests test4.nj + protml -D test5.ptn | njdist -w > test5.nj + @comparetests test5.nj + protml -D test15.ptn > test15.dis + @comparetests test15.dis + njdist test15.dis > test15.nj + @comparetests test15.nj + njdist -o 18 test15.dis > test15.njo + @comparetests test15.njo + njdist -o 18 -T test15.tree test15.dis > test15.njo + @comparetests test15.tree + @echo All $@ successfully done! + +clean: + rm -f *.comp *.test + rm -f protml.eps protml.tre + rm -f nucml.eps nucml.tre + rm -f njdist.eps njdist.tpl + +proper: + make clean + rm -f test4.tpl test4.ml test5.tpl test5.ml test15.tpl test15.ml test7.mls test7.tpl test7.mlq + rm -f test6.mls test6.tplq test6.mlq test6.tpl test6.ml + rm -f test4.dis test4.nj test5.nj test15.dis test15.nj test15.njo test15.tree.tre --- molphy-2.3b3.orig/debian/tests/test15.cns +++ molphy-2.3b3/debian/tests/test15.cns @@ -0,0 +1,9 @@ +( + { + ( (Homo,Xenopus), (Drosophil,Artemia) ), + ( (Saccharom,Candida), (Mucor,Absidia) ), + (Arabidops,Lycopersi) + }, + Sulpholob, + (Thermococ,(Thermopla,(Methanoco,Halobacte))) +); --- molphy-2.3b3.orig/debian/tests/test15.ptn +++ molphy-2.3b3/debian/tests/test15.ptn @@ -0,0 +1,121 @@ +15 409 test15.ptn +Homo +EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE +RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT +REHALLAYTLGVKQLIVGVNKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD +NMLEPSANMPWFKGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV +LKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKN +PPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPK +FLKSGDAAIVDMVPGKPMCVESFSDYPPLGFAVRDMRQTVAVGVIKAVD +Xenopus +EKHIKIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE +RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT +REHALLAYTLGVKQLIVGINKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD +NMLEPSPNMPWFKGTTLLEALDCILPPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKPGMVVTFAPVNVTTEVKSVEMHHEALTEAVPGDNVGFNVKNVSVKDVRRGNVAGDSKI +PPMEAGSFTAQVIILNHPGQIGAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDNPK +FLKSGDAAIVDMIPGKPMCVESFSDYPPLGFAVRDMRQTVALGVIKAVE +Drosophil +EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE +RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVQIDAAGTGISDQT +REHALLAFTLGVKQLIVGVNKMDSYSEARYEEIKKEVSSYIKKVGYAAVAFVPISGWHGD +NMLEPSTNMPWFKGKTLVDALDAILPPARPTDKALRLPLQDVYKIGGIGTVPVGRVETGV +LKPGTVVVFAPANITTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKA +PPKGAADFTAQVIVLNHPGQIANGYTPVLDCHTAHIACKFAEILEKVDRRSGKTTEENPK +FIKSGDAAIVNLVPSKPLCVEAFQEFPPLGFAVRDMRQTVAVGVIKAVN +Artemia +EKHINIVVIGHVDSGKSTTTGHLIYKCGSIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE +RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT +REHALLAYTLGVKQLIVGVNKMDSFSEARFEEIKKEVSAYIKKIDYAAVAFVPISGWHGD +NMLEASDRLPWYKGKTLLDALDAILPPSRPTEKPLRLPLQDVYKIGGIGTVPVGRVETGI +IKPGMIVTFAPANITTEVKSVEMHHESLEQASPGDNVGFNVKNVSVKELRRGYVASDSKN +PARGSQDFFAQVIVLNHPGQISNGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEAEPK +FIKSGDAAMITLVPSKPLCVEAFSDFPPLGFAVRDMRQTVAVGVIKSVN +Saccharom +EKHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGISGQT +REHALLAFTLGVRQLIVAVNKMDSWDESRFQEIVKETSNFIKKVGYKTVPFVPISGWNGD +NMIEATTNAPWYKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN +PPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPK +FLKSGDAALVKFVPSKPMCVEAFSEYPPLGFAVRDMRQTVAVGVIKSVD +Candida +EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYHVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT +REHALLAYTLGVKQLIVAVNKMDSWDKNRFEEIIKETSNFVKKVGYKTVPFVPISGWNGD +NMIEPSTNCPWYKGKTLLEAIDAIEPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGI +IKAGMVVTFAPAGVTTEVKSVEMHHEQLAEGVPGDNVGFNVKNVSVKEIRRGNVCGDSKN +PPKGCDSFNAQVIVLNHPGQISAGYSPVLDCHTAHIACKFDTLVEKIDRRTGKKLEENPK +FVKSGDAAIVKMVPTKPMCVEAFTDYPPLGFAVRDMRQTVAVGVIKSVE +Mucor +EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEEFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYNVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT +REHALLAFTLGFRQLIVAINKMDTWSQDRYNEIVKEVSGFIKKIGFKSVPFVPISGWHGD +NMLDESTNMPWFKGKTLLEAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGT +IKAGMVVNFAPAAVTTEVKSVEMHHETLTEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN +PAKESASFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFSELIEKIDRRSGKKMEDSPK +FVKSGDSAIVKMVPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE +Absidia +EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYHVTVIDAPGHRDFIKNMITGTSQADCGILIIAAGTGISGQT +REHALLAFTLGVRQLIVAINKMDSWSEQRFNEIIKEVSGFIKKIGFKSVPFVPISGWHGD +NMLEESTNMPWYKGKTLLDAIDAIDPPQRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKAGMVVTFAPANVTTEVKSVEMHHEQLVEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN +PAKEAGSFTAQVIVLNHPGQIGAGYAPVLDCHTAHIACKFAELLEKIDRRSGKKLEDAPK +FVKSGDSAIVKMIPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE +Arabidops +EKHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE +RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT +REHALLAFTLGVKQMICCCNKMDAYSKARYDEIIKEVSSYLKKVGYDKIPFVPISGFEGD +NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGM +IKPGMVVTFAPTGLTTEVKSVEMHHESLLEALPGDNVGFNVKNVAVKDLKRGYVASNSKD +PAKGAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKEIEKEPK +FLKNGDAGMVKMTPTKPMVVETFSEYPPLGFAVRDMRQTVAVGVIKSVD +Lycopersi +EKHISIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE +RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT +REHALLAFTLGVKQMICCCNKMDAYSKARYDEIVKEVSSYLKKVGYDKIPFVPISGFEGD +NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKPGMVVTFGPTGLTTEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGYVASNSKD +PAKGAASFTAQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKELEKEPK +FLKNGDAGMVKMIPTKPMVVETFAEYPPLGFAVRDMRQTVAVGVVKNVD +Sulpholob +QKHLNLIVIGHVDHGKSTLIGRLLMDRGFIDEKTVKEAEAAKKLGKSEKYAFLMDRLKEE +RERGVTINLSFMRFETRKYFFTVIDAPGHRDFVKNMITGASQADAAILVVSAKKGMSGQT +REHIILSKTMGINQVIVAINKMDLYDEKRFKEIVDTVSKFMKSFGFNKVKFVPVVAPDGD +NVTHKSTKMPWYNGPTLEELLDQLEIPPKPVDKPLRIPIQEVYSISGVGVVPVGRIESGV +LKVGDKIVFMPVGKIGEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN +PPTVADEFTAQVIVIWHPTAVGVGYTPVLHVHTASIACRVSEITSRIDPKTGKEAEKNPQ +FIKAGDSAIVKFKPIKELVAEKFREFPALGFAMRDMGKTVGVGVIIDVK +Thermococ +EKHINIVFIGHVDHGKSTTIGRLLFDTANIPENIIKKFEEMGEKGKSFKFAWVMDRLKEE +RERGITIDVAHTKFETPHRYITIIDAPGHRDFVKNMITGASQADAAVLVVAVTDGVMPQT +KEHAFLARTLGINNILVAVNKMDMYDEKKFKAVAEQVKKLLMMLGYKNFPIIPISAWEGD +NVVKKSDKMPWYNGPTLIEALDQMPEPPKPTDKPLRIPIQDVYSIKGVGTVPVGRVETGV +LRVGDVVIFEPASTIGEVKSIEMHHEPMQEALPGDNIGFNVRGVGKNDIKRGDVAGHTNN +PPTVVRPFKAQIIVLNHPTAITVGYTPVLHAHTLQVAVRFEQLLAKLDPRTGNIVEENPQ +FIKTGDSAIVVLRPTKPMVIEPVKEIPQMGFAIRDMGQTVAAGMVISIQ +Thermopla +QKHLNLITIGHVDHGKSTLVGRLLYEHGEIPAHIIEEYKEAEQKGKTFEFAWVMDRFKEE +RERGVTIDLAHRKFETDKYYFTLIDAPGHRDFVKNMITGTSQADAAILVISARDGVMEQT +REHAFLARTLGVPQMVVAINKMDAYSEKRYNEVKADAEKLLRSIGFKDISFVPISGYKGD +NVTKPSPNMPWYKGPTLLQALDAFKVPEKPINKPLRIPVEDVYSITGIGTVPVGRVETGV +LKPGDKVIFLPADKQGDVKSIEMHHEPLQQAEPGDNIGFNVRGIAKNDIKRGDVCGHLDT +PPTVVKAFTAQIIVLNHPSVIAPGYKPVFHVHTAQVACRIDEIVKTLNPKDGTTLKEKPD +FIKNGDVAIVKVIPDKPLVIEKVSEIPQLGFAVLDMGQTVAAGQCIDLE +Methanoco +TKILNVAFIGHVDAGKSTTVGRLLLDGGAIDPQLIVRLKEAEEKGKGFEFAYVMDGLKEE +RERGVTIDVAHKKFPTAKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVNVDDGIQPQT +REHVFLIRTLGVRQLAVAVNKMDTFSEADYNELKKMIDQLLKMIGFEQINFVPVASLHGD +NVFKKSERNPWYKGPTIAEVIDGFQPPEKPTNLPLRLPIQDVYTITGVGTVPVGRVETGI +IKPGDKVVFEPAGAIGEIKTVEMHHEQLPSAEPGDNIGFNVRGVGKKDIKRGDVLGHTTN +PPTVATDFTAQIVVLQHPSVLTDGYTPVFHTHTAQIACTFAEIQKKLNPATGEVLEENPD +FLKAGDAAIVKLIPTKPMVIESVKEIPQLGFAIRDMGMTVAAGMAIQVT +Halobacte +EQHQNLAIIGHVDHGKSTLVGRLLYETGSVPEHVIEQHEEAEEKGKGFEFAYVMDNLAEE +RERGVTIDIAHQEFSTDTYDFTIVDCPGHRDFVKNMITGASQADNAVLVVAADDGVQPQT +QEHVFLARTLGIGELIVAVNKMDLYGESEYKQVVEEVKDLLTQVRFENAKFIPVSAFEGD +NIAEESEHTGWYDGEILLEALNELPAPEPPTDAPLRLPIQDVYTISGIGTVPVGRVETGI +LNTGDNVSFQPSDVSGEVKTVEMHHEEVPKAEPGDNVGFNVRGVGKDDIRRGDVCGPADD +PPSVAETFQAQIVVMQHPSVITEGYTPVFHAHTAQVACTVESIDKKIDPSSGEVAEENPD +FIQNGDAAVVTVRPQKPLSIEPSSEIPELGFAIRDMGQTIAAGKVLGVN --- molphy-2.3b3.orig/debian/tests/test15.tree +++ molphy-2.3b3/debian/tests/test15.tree @@ -0,0 +1,5 @@ +(((((Homo:1.456,Xenopus:2.215):5.159,(Drosophil:5.257,Artemia:7.247):3.724) +:1.075,((Saccharom:5.073,Candida:4.014):2.615,(Mucor:4.444,Absidia:2.810) +:3.308):3.309):1.947,(Arabidops:1.604,Lycopersi:1.554):12.729):26.645, +Sulpholob:33.726,(Thermococ:23.040,(Thermopla:23.538,(Methanoco:22.576, +Halobacte:28.715):4.132):1.271):2.403); --- molphy-2.3b3.orig/debian/tests/test4.ptn +++ molphy-2.3b3/debian/tests/test4.ptn @@ -0,0 +1,13 @@ +4 90 test4.ptn +Data1 +MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMKPTLLTATSVFIIAFIHAPPVDK +DGHREPVSGSGRVINTWADIINRANLGMEV +Data2 +MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMKPTLLTATICFIIAFIHAPPVDK +DGHREPVAGSGRVISTWADILNRANLGFEV +Data3 +MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMKPTLLTATICFIVAFIHAPPVDK +DGHREPVAGSGRVINTWADVLNRANLGMEV +Data4 +MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMKPTLLAATACFVIAFIHAPPVDK +DGHREPVAGSGRVIATWADVINRANLGMEV --- molphy-2.3b3.orig/debian/tests/test5.ptn +++ molphy-2.3b3/debian/tests/test5.ptn @@ -0,0 +1,36 @@ +5 352 test5.ptn +Tabac_chl +MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI +DGIREPVSGSLLYGNNIISGAIIPTSAAIGLHFYPIWEAASVHEWLYNGGPYELIVLHFL +LGVACYMGREWELSFRLGMRPWIAVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF +NFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLIRETTENESANEGYRFG +QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGISTMAFNLNGF +NFNQSVVDSQGRVINTWADIINRANLGMEVMHERNAHNFPLDLAAIEAPSTN +Prochloro +MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFIIAFIAAPPVDI +DGIREPVAGSLMYGNNIISGAVVPSSNAIGLHFYPIWEAASMDEWLYNGGPYQLVVFHFL +IGIFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPLGQGSFSDGMPLGISGTF +NFMLVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETSENESQNYGYKFG +QEEETYNIVAAHGYFGRLIFQYASFNNSRALHFFLAAWPVVGIWFTSLGISTMAFNLNGF +NFNQSVMDSQGRVISTWADILNRANLGFEVMHERNAHNFPLDLAAVKAPSII +Anacystis +MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIVAFIAAPPVDI +DGIREPVAGSLMYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVVFHFL +IGVFCYMGREWELSYRLGMRPWICVAYSAPVAAATAVFLIYPIGQGSFSDGMPLGISGTF +NFMFVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQNYGYKFG +QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTSLGISTMAFNLNGF +NFNQSVLDSQGRVINTWADVLNRANLGMEVMHERNAHNFPLDLAAGEAPAIN +Fremyella +MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVIAFIAAPPVDI +DGIREPVAGSLIYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVIFHFL +LGCACYLGRQWELSYRLGMRPWICVAYSAPLASATAVFLIYPIGQGSFSDGMPLGISGTF +NFMIVFQAEHNILLHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTETESQNYGYKFG +QEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVVGIWFTALGVSTMAFNLNGF +NFNQSVIDSQGRVIATWADVINRANLGMEVMHERNAHNFPLDLAAGEAPAIN +Synechocy +MTTTQLGLQEQSLWSRFCCWITSTSNRLYIGWFGVLMIPTLLTATTCFIIAFIAAPPVDI +DGIREPIAGSLLYGNNIITAAVVPSSNAIALHFYPIWEAHSLDEWLYNGGPYQLNVFHFL +IGIFCYLGRQWELSYRLGMRPWICVAYSAPVAAATATLLIYSIGQGSFSDGLPLGISGTF +NFMLVLQAEHNVLMHPFHMLGVAGVFGGALFAAMHGSLVTSSLIRETTEVESQNQGYKFG +QEEETYNIVAAHGYFGRLIFQYASFNNSRALHSFLGAWPVVGIWFAALAVCCFAFNLNGF +NFNQSILDAQGRPVSTWADVINRANIGFEVMHERNVHNFPLDLASGDAPAIE --- molphy-2.3b3.orig/debian/tests/test6.nuc +++ molphy-2.3b3/debian/tests/test6.nuc @@ -0,0 +1,145 @@ +6 1344 test6.nuc +Chimp +TAAATCATCCCGCACCAAACCAACCAAACGATCCACTACCCCCTACATTCACACCCCTCC +TACGCTAGACACATCCAACAAATAATTCACACAAACCCCAACCCACTCAAATGCATCGAT +CCCCCACCAAACACTTCTACAAAATAAAGAAAAAACCTCTATAATCACCCAACCACCCAA +AAACTTATACACCAAGCACTCCCTACGCTAACCACAACACAACACAACCACCCACAAAAC +AATCTCACTTTACTCCCATTCATGACCACCCCACAAATCCACGAAAATCATACCCCCAAC +ACAATCCACAATCCAACAATTCCCCCCCACCCTCTCCTCCACACCCCATAATCATTCAAA +AAACATAACCCCCTACCCTCAGTACCCCCAAACAGGCCCCAACTACCATTAAACAACTAA +TACGCACATCTTGTAACAACCCATTCCCCTCCCACTACAACCCAAGTTACACTCCGATCG +ATTCCCGACCCACCACCGCGCTTCATATATCAAACCGAATAACCTCAGACCGTTACCACA +CCCCATGACCCTCAACTCCCAATTTAATTCGCACAACCCCACCACAACATCACCACATTC +CCAAGATTCCCTCCCCACGAACTTATACACATTCCCATTTTCAACCAATCCTATTCCAAA +AATATACGTATAAATCCAGTCGAACTATAAGACACCACTCCCTCACTTTTCCCAACCACT +ATCACTGAATCAACACAGTCTCCCATCACCTAAACAAACCGACCACCCACCCCCTAAAAT +ACCCAACCTCACCACACTCACACTCACATCCGCTCACACCCAGCCTCATGGCATCGCCCT +ACCAATCAACACATCCGAAAAAATCGTAACTTAAAACAAAAGCCACGAAATACCACCCAC +AACACAATAGATAGAATAATTTCTCAAATTCTCCTCCATCTCCCTACACCTCAACAAAAT +TTTTACCGAAACCATCGCCCCACTTCAACGTCTCAACGCCCCCTTTAACCTAATACCACC +CCCGACCCCCACCAATAAATTAACTCTTCAGCCATACCTTAATAAATTACAATTCAACAA +ACATCACACACTCCCAAAAACCCACAACTAACCTTACCCAAACTAACTAAACACTAAGCA +ATCCAACCATCCACGAATCCCAAAAATATCTACCAAACAAAACCTACAAAAAGCACCAAA +CTACCTAGCCTTATCCCCAATCCAAAATAGCAAAAATACCTAAACATCAAACACTTTCAC +TTTGTACCACAACCAATACACGTCCAAACAACACTCTGTATCACCCAGACATACTCCAAT +CCATTCACTAAACACATACTCTTA +Bonobo +TAAATCATCCCACACCAAACCAACCAAACGATTCACTACCCCCTACATTCACACCCCTCC +CACACTAGACACATCCAACAAATAATTCACACAAACCCCAATCCACTCAAACGCGTCAAT +CCCCCACCAAACACCTCTACAAAATAATGAAAATACCTCCATAATCACCCAACCACCCAA +AAACCCATACAACAAGCACTCCCTACGCTAACCACAACACAACACAACCACCCACAAAAT +AACCTCACTTTATTTCCATTCACGACCACCCCACAAATCCACGAAAATTACACCCCCAAC +ACAACCCGCAATCCAACAATTCCTCCCCACCCTCTCCTCCCCACCCCGCAATTACTTAAA +AAATATAATCCCCTACCCTCAATACCCTCAAGCAGGCCCCAACTACCATTAAACAACCAA +TATGCACATCTTATAACAACCTATCCCCTTCTCACTGCAACTCAAATCACACCCCGATCG +ATTCCCGACCTACCACCACACTTCATATATCAAACCCAATGACCTCAAACTGTTACCACA +CCCCGCGACCCTCAACTCCCAACTTAATTCACACAACTCCACCATAACATCACCACATTC +CCAAAATTCCCTCCCCATGAACTTATACACATTCCCATCTTCAACCAATCCTATTCAAAA +AACACACGTATAAATTCAGTTGAACTATAAAACACAACTCTCTCACTTTTCCCAACCGCT +ATCACTGAATCAACACAGCCTCCCGTCACTTAAACAAACCAACCATCCACCCCCCAAAAT +ACCCAACCTCACCATACTCACACTCACATCCACTCACACCCAACCTCGTAGCATCGCCTT +ACCAATCAACACACCCAGAAAAATCATAACTTAAAACAAAAGCCACGGAGTACCACCCGC +AACGCAATAGATAGAATAACCTCTCAAATTCTTCTCCATCTCCCCACGCCTCAACAAAAT +TTTTACCGAAACCATCGCCCCACTTCTATATCTTAACGCCCCCTTTAACCTAATACCACC +CCCAACCCCCACCAATAAACCAACTCTTCGGCCATACCTTAATAAATTACAATCCAACAA +ACATCACACACTCCCAAAAACTCACAACTAACCTTACCCAGACCAACTAAACACTAAGCA +ATCCAACCATCTACTAATTCCAAAAACATCTACCAAACAAAACCTACAAAAAGCACCAAG +CTACCTAGTCCTATCCCCAATCCAAAATAGCAAAAATACCTAAACATCAAACATTTTCAT +TTCATATCACAACCAATACACGTCCAAACAACACTCTGTATCACCCAGACATACTCCAAT +CCATCCACTAAACACATACTCTTA +Human +TAAACCACCCCACACCAAACCAACCAAATAATCCACTACCCTCTACATTCGCACCCCTCC +TACACCAGACGCATTCAACAAACGATTTATACAAACTTCAATCCGTCCGAACACACTAAT +CCCCTACCAAACACTTCTACAAAACAATAAAAAAACCTCCACAGTCACCTGACCGTTCAA +AAACCCACACACTCAACACTCCTCACACCAACTATAACGCGACACAACCATCCAAAAAAT +AGCCTCACTTTATTTTCATTCACAACCACCCCGCAAATCCACGAAAAACATACCCCCAAC +GCGACCTGCAGCTCAACAACTCCCCCCCACCCCCTCCCCCACACCCCACAACCATCCAAA +AAGTATAACCACCCACCCTCGACATCCTTAAACAGGCCCTAACTACCACTAAACAACCAA +TACACATACCTTACGGCGACCTATCCCCCCTCCACTATAACCCAAACCACACTCCAATCA +ACTCCTGGTCCACCACCACATCTCACGCATTAGGCAAAATAACCTCAAGCCCCTACCACA +CCCCACAATCCTCAGCCTCCAATCTAACTCACACAGCCCCACCACAACATCATCACATTC +CTAAAACCCCCCCCCCCCAAACCTACACACATCTCTATTTTCAACCAACCTTATCCCAAA +AATACATGCATGAATCCAGTCGAACTATAAAACACAAATCCCTCACCTCCCCCAATCACC +ACCACTGAATTAGCACAACCTTCCATCGTCTAAACAAACCAACCGCCTACCCCTCAAAAT +ATCCAACCTCATCACACCCACACCCACTCTCACCCATATCCAACTCCACAGCATCGCCCT +ACCAACCAATACACTTAAAAAAATCGTAACCTGGAACAAAAACCACGGAATACCACCCAC +AACACAATAGATAGAATAACTTCTCAAGTCCTTTCCCACTCTCCCACGTCTCAACAAAAT +TTCCACTGAAACCATCGCCCCACCCCCACACCTCAACGCCTCCTCCAATCCAGCACCGCC +CCCAACCCCCATCAACAAACCGACTCTCTAAACGTACCTTAATAAACCGCAATCCAACAA +ATATCATACACTCCTAAGGACCTACTACTAACCTCGCCCAAATCAACTAAGCATCAAGCA +ATTCAGCCATCCACTAACCCCAAAAACACCCATCAAGCAAAATTCACAAAAAGCACCAAG +CTATCTAGCCCCATCCCCAACCCAAAACAACAAAGACACCTAAACATTAAACACTTTCAT +CCCACGTCATAACCAATACACGCCCAAGCAGTACTCTGTATCACCCAAACATACTCCAAT +TCACCCACTAAACGCACACTCTTA +Gorilla +TATATTATCCCACGCCGAACCGACCGAACAATTCATCACCCTCTACATCCGCACCCCTCC +CACTTTAAACCCATTCAACAAACAATTCACACAAATCCCAACCCATCCAAATACACCAAC +CCCCCACCAAACACTCTTACAAAGCAATATAAAAACCTCCAGAACCACCCAGTCACCCAA +AAACTGACACATCGAATACTCCTTACACCAACCACAACATAACGTAACCACCTAAAAAAT +AATCTTATTTTGCTTTCCTTCACAACCACCCCACAAATTTATAGAAAATACCCCCCCAAT +ACAACCCACAGTTCAACAATCCCTCCCTGCCCCCCCCTCTACATCCCTCAAACACCCAGA +AAGCATTACTCCCTATCACCCATACCCCCAAATAGGCCCCAACTACTATTAAATAACCAA +TACACACATCTTAAATTAACCTATCTCCTTTCCACTGCAATCCAAGTCACACTCCGAACA +ATTCCCGACCCACCACCACTCTTCATGCACTAAACCAGTTGACCTCAAATTCCCATTACA +CTTCACAACCCTTAGCCCCTAACCTAACCCACACAACTCCACCACAACATTATCAAATTA +TCAAAACTCCCCCTCCACAAATTCACACACATTACCATCTACAACCAACCCTATTCCAAA +AACATATACATAAATTCGATTGACCCATAAAACATAACCCCCTCACCTCCCCCAACCACT +ACTATTCAATCAGCACAGCTTCCTACCACCCAAACGAATCGGCCATCCATCCCTCATAAT +GCCCAGCTTCATCACACCTATACCCACCTCCACTCTTACCCAACTTCATAACATCGCCCT +ATTAATCGACGCACTCAAAAAAATTACAACCCAAAACAACAACCATGGAGTACTACTTAT +AGTATAGTAGATAGAATAACTTTTCAAAACCTTTTCCACTTCCCCACGCCTCAACAAGAT +CCCCACCAAAGCCACCGCTTCACGCCCATAACCTGATACTCCCCTCAACTCAACACCACC +CTTAGCTCCTACCAACAAATCAACTCCCCAACTATACCCTAATACATCACAATTCAACAA +ACACCGCGCACACCCAAAAACCCGCAACTACCCTTGCTTAGACCAACTAAACACCAAGCG +ATCCAGCCATCAACCAATCTCAAATACATCCACCAAATAAAACCTACAAAAAGCACCAAA +TCATCTAGCCCCATCCCCAGTCCAGAACAACAAAAATATCCGAACACTGAAAATTTTCAC +CCCACGCCACAATCGATACGCACCCGAACAATACTCCGTATCACCAAAACCTACTCTAAC +CTACCCACCAAACATACACTCCTA +Orang +TAAACCACCCCACGCCAAATCGACCAAAAAACCCACTACTCTCAACATCCATACCCCCCC +CACATTAAGCCCACTCAGCAAACACTCCACACAAACCCCAACTCATCCAAACACATCAAC +CCCCCATCAGACACTCCCATATAATACCAAAAAAACCCCCACAACCAACCAACCACCTAA +AAACCTATACAACAAACACCCCCCATATCGACCACAACACAACACGACCACTCAAAAAAA +ACCCACCTCCCACCTTCGATCACATCCACTCCACAGACCCACAGAAAACACAACAACAGC +GCAACCCACAATCTGACAACCTTTTCACACTCTCCCCCCCACATCCCACAACCGTCCAAA +AAACATAACCTCCCACTCTCCATATCCTCCACCAAGCCCCGACCGCCATTAGACGGCCAA +TTCACTCACCCTTTAACACCCCATTCTTCTCCCACTACAATTCGCGCAATACTCCAAGCG +ATCCTTGACGCATCACCACCCCCCCAACTTTAAGCAAAGCAACTACAAACCTCAACTACG +ACCTACAACTCATAGTCTCTAATTTAACTAACATATCCCCAACGCAACATCCCCACACTC +CCAAAACCCATTACTCGTATGTTCACACACATCCCTACCTCCAATCCACCCCAACCCAAA +AATGTACACACACATTCGTTCAACCCACAAGACGCAACCCCCTCATTCCCCCCAATCACT +ACCACCTAATCACCACAACTCCCCACCAACCAGACAAACCAACTACCTACCTCCCAAAAT +ACCCAACCCCGCAACACCCACGCTTATCCCCATCCATACCCGATCTCAATACACCCTCCC +ATCAATTAACACATCCAAATAAATCATAACTCAAAACAATAATCACAGGACACCACCTGT +AACCTAACAGGCAAGATAACTCTTCAAAGCCTCCCCCACCCACCCACGCCTCAACAGACC +CTCCATCAGAATTATCAACCCATACCCATACCCCAACACCCTCCCTAACCTAGCACCGTT +CTCAGCCCTCGCAAACAAACCTACACCCTAACCACACCTCAACACACCGCAACCCAACGA +ACACCACACACACTCAAAAATTCACAACTATCCCTGTCCAAACCAACCAAACACTAAGCA +ATCCAGCCCCTAATTAACCCCGAAAACACCCACCAAATCAAACCCACAAAAAGCCCTATA +CCATCCAACTCCATCCCCTATCCGAAACACCAAAAACCTCTAAATACAAAACACTTCCAC +CCCACCCCATAATCGACACATAACCAAACGACGCACCGCATCATCCGAATCCACCCCAAT +TTACTTTTTAGACACACACCCCTA +Siamang +CAAATCACCCTACACCAAGCCGACCGCACAACTTACTATCTTTCACATCCATACCCCACT +TATACTCATCACACCCAACAAACGACTCACAAAAACTCCAACTTGTCCAAACACACTAAC +CCTTCATCAAACACCTCCACAAAACAACACAAAAACCCCCACAACTAATCCACCAACCAA +AAACTCATACACCAAACACCCCATATATCAACCACAACACAACATGACCACCTACAAACA +TACCACCCTCCATCCCAAACTACAACCATCCCACAAACCCACAACAAACACACCAAAAAG +ATAACCCACAGTCTAGCAACTTCTCATTACCCCTCCACCCACACCCCACAACTACCTAAA +AAATACAACATCCCACTCCCTTCAACCACACTCAAGCCCCGACCACTATTAAACGATCAA +CACACACACCTCACAATACCTCGCTCCTTCCCAACCGCCACTCAAACTGTGCTCCAACTA +ACACCCGACTTATCACCGTTTCTCAAGTCCCAAACCCAAAAACTCAGAACTCCAACTTTA +CTTTACGTAAATCAGTTCCTTACCCAACATACATAATCTCACCATAACACTCCAATACTC +CCAAAACTCCCCTCTCATAAACCTATACACGTTCCCATCTTCAACCAATACCATCCGAAG +GACATACACACAAATCCATCTCACCTATAACGCACAACTTACCCATTCTCTTCAATCGCC +ACCATCCAACTAACACACCTCCTAAGCATTCAAATAAGCTATCCACTCACTCCTCACAAC +ACTCAACCCCACCACGCCTATACTCATCCCTATAAACACCTAACCCCGCAATATTCCCTT +ACTCACCACTGCATCTAAAAAAATCACAGTCCAGAACAACAGCCTCAGGGCACAATTCAT +AGCCTAATAGATATAACAACTACTCAAAACTCCCTCCACTCTCCCACATCCCAACAAAAC +CTTTGCCAGAACCAACATTTTATATCCACCCCTCAACACCCCCTTCGACTTGACACCATA +CCTGACCTTCAAAAATAAGGCTACTACCCAATTATACTCTAATAAACCACAATCCCATTA +GTTCCACACACACCCACAAACCCACAACTGCCTCTAGTTAAATCAACCGAGTATCAAGCA +ACCCGATACCAAATCAACCCAAAAAACGCCTACCCAACACTACCCCCAACAAGCACCAAA +TTATCCAATTTCACCCCTAATCCAAAATAGCAAAAAAACCTAAACACCAATTATTCTTAT +CCTCCACCACAACCGACACACAATCAAACTGCATATCACACTTTCTACACATGCCTCAAT +CCATCTATCACGCACAAATATTAA --- molphy-2.3b3.orig/debian/tests/test7.ptn +++ molphy-2.3b3/debian/tests/test7.ptn @@ -0,0 +1,57 @@ +7 409 test7.ptn +Homo +EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAEMGKSFKYAWVLDKLKAE +RERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGISGQT +REHALLAYTLGVKQLIVGVNKMDSYSQKRYEEIVKEVSTYIKKIGYDTVAFVPISGWNGD +NMLEPSANMPWFKGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV +LKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKN +PPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPK +FLKSGDAAIVDMVPGKPMCVESFSDYPPLGFAVRDMRQTVAVGVIKAVD +Drosophil +EKHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAQEMGKSFKYAWVLDKLKAE +RERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVQIDAAGTGISDQT +REHALLAFTLGVKQLIVGVNKMDSYSEARYEEIKKEVSSYIKKVGYAAVAFVPISGWHGD +NMLEPSTNMPWFKGKTLVDALDAILPPARPTDKALRLPLQDVYKIGGIGTVPVGRVETGV +LKPGTVVVFAPANITTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKA +PPKGAADFTAQVIVLNHPGQIANGYTPVLDCHTAHIACKFAEILEKVDRRSGKTTEENPK +FIKSGDAAIVNLVPSKPLCVEAFQEFPPLGFAVRDMRQTVAVGVIKAVN +Saccharom +EKHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGISGQT +REHALLAFTLGVRQLIVAVNKMDSWDESRFQEIVKETSNFIKKVGYKTVPFVPISGWNGD +NMIEATTNAPWYKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKN +PPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPK +FLKSGDAALVKFVPSKPMCVEAFSEYPPLGFAVRDMRQTVAVGVIKSVD +Mucor +EKHVNVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEEFKEAAELGKSFKYAWVLDKLKAE +RERGITIDIALWKFETPKYNVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGTGISGQT +REHALLAFTLGFRQLIVAINKMDTWSQDRYNEIVKEVSGFIKKIGFKSVPFVPISGWHGD +NMLDESTNMPWFKGKTLLEAIDAIEPPVRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGT +IKAGMVVNFAPAAVTTEVKSVEMHHETLTEGLPGDNVGFNVKNVSVKDIRRGNVCSDSKN +PAKESASFTAQVIILNHPGQISAGYAPVLDCHTAHIACKFSELIEKIDRRSGKKMEDSPK +FVKSGDSAIVKMVPSKPMCVEAYTDYPPLGFAVRDMRQTVAVGVIKAVE +Arabidops +EKHINIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE +RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT +REHALLAFTLGVKQMICCCNKMDAYSKARYDEIIKEVSSYLKKVGYDKIPFVPISGFEGD +NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGM +IKPGMVVTFAPTGLTTEVKSVEMHHESLLEALPGDNVGFNVKNVAVKDLKRGYVASNSKD +PAKGAANFTSQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKEIEKEPK +FLKNGDAGMVKMTPTKPMVVETFSEYPPLGFAVRDMRQTVAVGVIKSVD +Lycopersi +EKHISIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFKEAAEMNKSFKYAWVLDKLKAE +RERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDSTTGISGQT +REHALLAFTLGVKQMICCCNKMDAYSKARYDEIVKEVSSYLKKVGYDKIPFVPISGFEGD +NMIERSTNLDWYKGPTLLEALDQINEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGV +IKPGMVVTFGPTGLTTEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGYVASNSKD +PAKGAASFTAQVIIMNHPGQIGNGYAPVLDCHTSHIAVKFSEILTKIDRRSGKELEKEPK +FLKNGDAGMVKMIPTKPMVVETFAEYPPLGFAVRDMRQTVAVGVVKNVD +Sulpholob +QKHLNLIVIGHVDHGKSTLIGRLLMDRGFIDEKTVKEAEAAKKLGKSEKYAFLMDRLKEE +RERGVTINLSFMRFETRKYFFTVIDAPGHRDFVKNMITGASQADAAILVVSAKKGMSGQT +REHIILSKTMGINQVIVAINKMDLYDEKRFKEIVDTVSKFMKSFGFNKVKFVPVVAPDGD +NVTHKSTKMPWYNGPTLEELLDQLEIPPKPVDKPLRIPIQEVYSISGVGVVPVGRIESGV +LKVGDKIVFMPVGKIGEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN +PPTVADEFTAQVIVIWHPTAVGVGYTPVLHVHTASIACRVSEITSRIDPKTGKEAEKNPQ +FIKAGDSAIVKFKPIKELVAEKFREFPALGFAMRDMGKTVGVGVIIDVK --- molphy-2.3b3.orig/debian/FORMAT +++ molphy-2.3b3/debian/FORMAT @@ -0,0 +1,226 @@ + + Format of Input SEQUENCES File + + + standard MOLPHY input sequence data format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +4 90 +Data1 +MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMKPTLLTATSVFIIAFIHAPPVDK +DGHREPVSGSGRVINTWADIINRANLGMEV +Data2 +MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMKPTLLTATICFIIAFIHAPPVDK +DGHREPVAGSGRVISTWADILNRANLGFEV +Data3 +MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMKPTLLTATICFIVAFIHAPPVDK +DGHREPVAGSGRVINTWADVLNRANLGMEV +Data4 +MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMKPTLLAATACFVIAFIHAPPVDK +DGHREPVAGSGRVIATWADVINRANLGMEV +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Note, "~~~" is file separater. + +An input file has two parts of data; SIZE and SEQUENCES. + +1. SIZE +The first line of the file contains the number of species(OTUs) and the length +of amino acid sequences, in free format, separated by blanks(space or tab). +You can write comment of the data after two digits numbers, +separated by blanks. + +2. SEQUENCES +The following lines give sets of species name and amino acid sequence data. +Names are made up of letters and digits; the first character must be a letter. +The underscore "_" is regarded as a letter. Upper case and lower case letters are +distinct, so "spc_1", "Spc_1" and "SPC_1" are three different names. +Name can NOT include blanks. +You must put the amino acid sequence AFTER NEWLINE in free format. +Separated by whitespace(space, tab or newline) is allowed. +The amino acids must be specified by the one letter codes adopted by +IUPAC-IUB Commission on Biochemical Nomenclature (1968). + + CODE Amino acid Description + A Ala Alanine + R Arg Arginine + N Asn Asparagine + D Asp Aspartic acid + C Cys Cysteine + Q Gln Glutamine + E Glu Glutamic acid + G Gly Glycine + H His Histidine + I Ile Isoleucine + L Leu Leucine + K Lys Lysine + M Met Methionine + F Phe Phenylalanine + P Pro Proline + S Ser Serine + T Thr Threonine + W Trp Tryptophan + Y Tyr Tyrosine + V Val Valine + B Asx Aspartic acid or Asparagine + Z Glx Glutamine or Glutamic acid + X Xaa Any amino acid + - gap Ins/Del + + + Felsenstein's PHYLIP "SEQUENTIAL" format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 4 90 +Data1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFII +AFIAAPPVDIDGIREPVSGSGRVINTWADIINRANLGMEV +Data2 MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFII +AFIAAPPVDIDGIREPVAGSGRVISTWADILNRANLGFEV +Data3 MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIV +AFIAAPPVDIDGIREPVAGSGRVINTWADVLNRANLGMEV +Data4 MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVI +AFIAAPPVDIDGIREPVAGSGRVIATWADVINRANLGMEV +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +The information for each species follows, starting with a TEN-CHARACTER +species name (which CAN include punctuation marks and blanks). +You must use SEQUENTIAL_FILE with "-S" Switch, follow as: + + protml -S SEQUENTIAL_FILE + + + MOLPHY and PHYLIP common format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 4 90$ +Data1 $ +MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFIIAFIAAPPVDI$ +DGIREPVSGSGRVINTWADIINRANLGMEV$ +Data2 $ +MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFIIAFIAAPPVDI$ +DGIREPVAGSGRVISTWADILNRANLGFEV$ +Data3 $ +MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIVAFIAAPPVDI$ +DGIREPVAGSGRVINTWADVLNRANLGMEV$ +Data4 $ +MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVIAFIAAPPVDI$ +DGIREPVAGSGRVIATWADVINRANLGMEV$ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Note, '$' is newline(return) code. + + + PHYLIP and other packages "INTERLEAVED" format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 4 90 +Data1 MTAILERRESESLWGRFCNWITSTENRLYIGWFGVLMIPTLLTATSVFII +Data2 MTTALRQRESANAWEQFCQWIASTENRLYVGWFGVIMIPTLLTATICFII +Data3 MTTALQRRESASLWQQFCEWVTSTDNRLYVGWFGVLMIPTLLTATICFIV +Data4 MTTTLQQRSRASVWDRFCEWITSTENRIYIGWFGVLMIPTLLAATACFVI + +AFIAAPPVDIDGIREPVSGSGRVINTWADIINRANLGMEV +AFIAAPPVDIDGIREPVAGSGRVISTWADILNRANLGFEV +AFIAAPPVDIDGIREPVAGSGRVINTWADVLNRANLGMEV +AFIAAPPVDIDGIREPVAGSGRVIATWADVINRANLGMEV +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +You must use INTERLEAVED_FILE with "-I" Switch, follow as: + + protml -I INTERLEAVED_FILE + + + + Format of USERS TREES File + + standard USERS TREES file format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +3 +(((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA); +((HUMAN,((CHIMP,PYGMY),GORIL)),ORANG,SIAMA); +(((HUMAN,GORIL),(CHIMP,PYGMY)),ORANG,SIAMA); +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Note, "~~~" is file separater. + +An input file has two parts of data; SIZE and MACHINE READABLE TREES. + +1. SIZE +The first line of the file contains the number of machine readable trees. +You can write comment of the trees after one digits number, +separated by blanks(space or tab). + +2. MACHINE READABLE TREES +The following lines give sets of (user-defined) machine readable tree. +The tree is specified by the nested pairs of parentheses, enclosing names +and separated by commas. Semicolon ";" is tree terminator. +The pattern of the parentheses represents the tree topology by having +each pair of parentheses enclose all the members of a monophyletic group. +You must put the next machine readable tree AFTER NEWLINE in free format, +allow separated by whitespace(space, tab or newline). +for example, + + (((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA); + + ( + ( + ( + HUMAN, + ( + CHIMP, + PYGMY + ) + ), + GORIL + ), + ORANG, + SIAMA + ); + +the above two machine readable tree are the same. + +Note that the machine readable tree is an UNROOTED one, and therefore its base +must be multifurcation with a multiplicity of greater than or equal to three. + + Unrooted tree (PROTML & DISTNJ) Rooted tree (not allowed) + variable rate constant rate + + ( subtree1, subtree2, subtree3 ); ( subtree1, subtree2 ); + + :-----subtree1 + : :-----subtree1 + :-----subtree2 : + : :-----subtree2 + :-----subtree3 + ^root + ^provisional root + + + + Format of CONSTRAINED TREE File + + + standard CONSTRAINED TREE file format: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +( { HUMAN,CHIMP,PYGMY,GORIL }, ORANG, SIAMA ); +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Note, "~~~" is file separater. + +CONSTRAINED TREE file allow constrained machine readable tree. +Pair of PARENTHESIS indicates FIX tree structure, but Pair of BRACE indicates +COMBINATION tree structure in a monophyletic group. + +above CONSTRAINED TREE input PROTML with "-e" switch + + protml -e sequence_file constrained_tree + +automatic generation of all possible trees. +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +15 +(((HUMAN,(CHIMP,PYGMY)),GORIL),ORANG,SIAMA); +((HUMAN,((CHIMP,PYGMY),GORIL)),ORANG,SIAMA); +(((HUMAN,GORIL),(CHIMP,PYGMY)),ORANG,SIAMA); +((((HUMAN,PYGMY),CHIMP),GORIL),ORANG,SIAMA); +((((HUMAN,CHIMP),PYGMY),GORIL),ORANG,SIAMA); +((HUMAN,(CHIMP,(PYGMY,GORIL))),ORANG,SIAMA); +((HUMAN,((CHIMP,GORIL),PYGMY)),ORANG,SIAMA); +((((HUMAN,GORIL),PYGMY),CHIMP),ORANG,SIAMA); +((((HUMAN,CHIMP),GORIL),PYGMY),ORANG,SIAMA); +(((HUMAN,CHIMP),(PYGMY,GORIL)),ORANG,SIAMA); +((((HUMAN,GORIL),CHIMP),PYGMY),ORANG,SIAMA); +(((HUMAN,(PYGMY,GORIL)),CHIMP),ORANG,SIAMA); +(((HUMAN,(CHIMP,GORIL)),PYGMY),ORANG,SIAMA); +(((HUMAN,PYGMY),(CHIMP,GORIL)),ORANG,SIAMA); +((((HUMAN,PYGMY),GORIL),CHIMP),ORANG,SIAMA); +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --- molphy-2.3b3.orig/debian/PROTMLver1.DOC +++ molphy-2.3b3/debian/PROTMLver1.DOC @@ -0,0 +1,682 @@ + + PROTML version 1 ( old version ) + Maximum Likelihood Inference of Protein Phylogeny + + + Jun Adachi 1) and Masami Hasegawa 2) + + + 1) Department of Statistical Science, + The Graduate University for Advanced Study + 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan + + 2) The Institute of Statistical Mathematics + 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan + + + + INTRODUCTION + + + PROTML is a PASCAL program for inferring evolutionary trees +from protein (amino acid) sequences by using maximum likelihood. + + A maximum likelihood method for inferring trees from DNA or +RNA sequences was developed by Felsenstein (1981). The method +does not impose any constraint on the constancy of evolutionary +rate among lineages. He wrote a program (DNAML) implementing the +method, and included it in his program package, PHYLIP. The +program has been used extensively and has proved of great use in +phylogenetic studies (Hasegawa and Yano, 1984a; Hasegawa et al., +1985, 1990a; Hasegawa and Kishino, 1989; Kishino and Hasegawa, +1989; Zillig et al., 1989; Hasegawa, 1990, 1991; Golenberg et +al., 1990; Adkins and Honeycutt, 1991; Doebley et al., 1991; +Edwards et al., 1991; Les et al., 1991; Ruvolo et al., 1991; +Disotell et al., 1992; Lockhart et al., 1992). Computer +simulations have demonstrated that the method is highly efficient +in estimating a true tree under various situations such as a +violation of rate constancy among lineages (Hasegawa and Yano, +1984b; Hasegawa et al., 1991). + + DNAML, however, is confined to DNA or RNA sequence data, and +is not applicable to protein sequence data. In phylogenetic +studies of deep branchings, such as those among the three major +kingdoms of eukaryotes, archaebacteria and eubacteria, and those +in the early evolution of eukaryotes, ribosomal RNA sequence data +has been used widely (e.g., Woese, 1989; Sogin et al., 1989). In +spite of many works on the ribosomal RNAs, the universal root of +all contemporary organisms on the earth including eukaryotes, +archaebacteria and eubacteria remained uncertain. Miyata and his +coworkers demonstrated the usefulness of using amino acid +sequence data encoded by duplicated genes (duplicated prior to +the divergence among the major kingdoms) in establishing the +universal root (Iwabe et al., 1989; Hasegawa et al., 1990b; +Miyata et al., 1991). Furthermore, an evolutionary tree inferred +from ribosomal RNA data is sometimes misleading when base +composition differs widely among lineages, and a tree inferred +from protein sequences is more reliable in such cases (Loomis and +Smith, 1990; Hasegawa et al., 1993). + + Because no program was available for inferring a protein +tree by maximum likelihood based on a reasonable model of amino +acid substitutions, many authors used DNAML in analyzing +protein-encoding DNA sequences. As is well known, the third +position of codons evolve more rapidly than other positions, and +therefore DNAML was designed so that a user could specify the +relative rates of substitutions in several categories of +positions. This approach seems to be good in many cases when one +is interested in phylogenetic relationships among closely related +species. + + Even if the rate difference among positions in a codon are +taken into account, however, inclusion of the third positions in +the analysis can sometimes be misleading when the pattern of +codon usage differs among lineages. Furthermore, the assumption +(in DNAML) of independent evolution among three positions of a +codon can be a serious defect when one is interested in tracing +deep branchings, because a (negative) selection is likely to be +operating at the codon level, rather than at the individual sites +in the codon. Even if nucleotide frequencies of protein-encoding +genes differ among lineages, amino acid frequencies may not +differ significantly (Adachi and Hasegawa, 1992). Therefore, if +the amino acid substitution process can be represented by an +appropriate model, it seems to be better to handle amino acid +sequences rather than nucleotide sequences in estimating orders +of deep branchings from data of a protein-encoding gene, and +there is an increasing demand for a maximum likelihood program to +infer protein phylogenies. + + Kishino et al. (1990) developed a maximum likelihood method +for inferring protein phylogenies that takes account of unequal +transition probabilities among pairs of amino acids by using an +empirical transition matrix compiled by Dayhoff et al. (1978), +and the model is called the Dayhoff model (Hasegawa et al., +1992). Although the transition matrix was constructed from a +limited data set (accumulated up to 1978) of proteins encoded in +nuclear DNA, the Dayhoff model is not necessarily specific only +to those proteins, but is appropriate in approximating the amino +acid substitutions of wider protein species including +mitochondrial ones (Hasegawa et al., 1993; Adachi and Hasegawa, +1992; Adachi et al., 1992). + + The original program for private use in Kishino et al. +(1990), Mukohata et al. (1990), Hasegawa et al. (1990b), Iwabe et +al. (1991), and Miyata et al. (1991) was written in FORTRAN and +the number of species in the maximum likelihood analysis was +confined to five. In writing this program "PROTML" for public +use, we took advantage of another computer language, PASCAL, to +represent the tree structure of the data. In this program, there +is no limit on the number of species, provided the computer is +big enough. + + Since the number of possible tree topologies increases +explosively as the number of species increases (Felsenstein, +1978a), it is a serious problem to find the best tree among the +huge number of alternatives. We have developed a novel algorithm +for searching tree topologies, called "star decomposition", which +seems to be effective in finding the best tree. + + The parsimony method has been used widely in molecular +phylogenetics, but it may be positively misleading when the +evolutionary rate differs among lineages (Felsenstein, 1978b). +PROTML has proved of great use in inferring evolutionary trees +even in such situations (Hasegawa et al., 1992), and has been +applied to several phylogenetic problems (Hasegawa et al., 1993; +Adachi and Hasegawa, 1992; Adachi et al., 1992; Hashimoto et al., +1993). + + The overall structure of PROTML is similar to that of +Felsenstein's DNAML. We owe very much to DNAML in the writing +PROTML, and have adopted several fundamental routines from the +DNAML program. Furthermore, the input format of PROTML is quite +similar to that of DNAML. Features where PROTML differs from +DNAML (up to version 3.4) are as follows: + + (1) Amino acid sequence data are analyzed based on Dayhoff's + model(1978). + (2) The likelihood of multifurcating trees can be estimated. + (3) A novel method of topology search ("star decomposition") + is adopted. + (4) The Newton method is adopted in the maximization of + likelihood. + (5) Bootstrap probabilities of candidate trees can be + estimated. + + + + ALGORITHM FOR TOPOLOGY SEARCH + + Topological Data Structure + + Felsenstein considered a data structure representing the +unrooted tree, where each internal node (excluding external nodes +or tips) is decomposed into elements, the number of which +coincides with those of branches stemming from the node. The +elements are connected circularly through the pointers. + + By adopting such a data structure, we can store a partial +likelihood of a sub-tree stemming from the node. This means that, +when we estimate the likelihood of the tree, we need not +calculate likelihood through iteration of a loop by the times of +the number of nodes in revising the estimate of each branch +length, but need only revise the partial likelihoods of two nodes +of each branch. + + We extend this data structure so that a multifurcating tree +can be represented. Since branches are connected dynamically by +pointers, the data structure can easily be revised when a +different tree topology is adopted, and furthermore not only +bifurcating trees but also multifurcating trees can be +represented quite easily. The extreme limit of a multifurcating +tree is the star-like tree. + + + Automatic Topology Search by Star Decomposition + + The straightforward approach to inferring a tree would be to +evaluate all possible tree topologies one after another and pick +the one which gives the highest likelihood. This would not be +possible for more than a small number of species, since the +number of possible tree topologies is enormous (Felsenstein, +1978a). + + The strategy that Felsenstein's DNAML employs is as follows: +the species are taken in the order in which they appear in the +input file. The first three are taken and an unrooted tree is +constructed containing only those three. Then, the fourth species +is taken, and it is evaluated to see where it might best be added +to the tree. All possibilities (bifurcating trees) for adding the +fourth species are examined. The best one under the likelihood +criterion is chosen to be the basis for further operations. Then +the fifth species is added, and again the best placement of it is +chosen, and so on. At each step, local rearrangements of a tree +are examined. This procedure is continued until a bifurcating +tree connecting all the species is obtained (Felsenstein, 1992). + + The resulting tree from this procedure generally depends on +the order of the input species. Hence, Felsenstein recommends +performing a number of runs with different orderings of the input +species. + + The alternative strategy which we employ in the automatic +and semi-automatic search options of PROTML is called "star +decomposition". This is similar to the procedure employed in the +neighbor-joining method using a distance matrix (Saitou and Nei, +1987). This method starts with a star-like tree. Decomposing the +star-like tree step by step, we finally obtain a bifurcating tree +if all multifurcations can be resolved with statistical +confidence. Since the information from all of the species under +analysis is used from the beginning, the inference of the tree +topology is likely to be stable by this procedure. + + Let be the number of species under analysis. At first, a +star-like tree containing species is constructed. Then, a pair of +species is separated from others. Among all possible pairwise +combinations of species, a pairing that gives the highest +likelihood is chosen. The resulting tree can be regarded as a +star-like tree with groups (a single species may form a group), +if the selected pair is regarded to form a group. This procedure +is continued until all multifurcating nodes are resolved into +bifurcating ones. + + When the information content of the data is not large enough +to discriminate among alternative branching orders, it might be +misleading to resolve all the multifurcations into bifurcations. +Hence, by using "Akaike Information Criteria (AIC)" (Akaike, +1974), the program decides whether the multifurcation should +further be resolved or not. + + + + PROTML USER'S GUIDE + + Options + + The program allows various options that alter the amount of +information the program is provided or what it is to be done with +the information. The program is notified that an option has been +invoked by the presence of one or more letters after the last +number on the first line of the input file. These letters may or +may not be separated from each other by blanks, though it is +usually necessary to separate them from the number by a blank. +They can be in any order. Thus to invoke options U, W and B, the +input file starts with the line: + + 19 409 UWB + +or + + 19 409 W U B + + This program has three mode of topology search; i.e., +Automatic mode, Semi-automatic mode and User tree (manual) mode. + + Automatic mode. + Unless specified otherwise, the procedure uses automatic mode, + so it starts with a star-like tree. + + "S" : Semi-automatic mode. + Semi-automatic mode starts with a multifurcating tree that a + user designates. + + "U" : User tree mode. + User tree (manual) mode is similar to the "U" option in + Felsenstein's DNAML. This mode calculates the likelihood of + all user defined topologies. Different from DNAML, this + program allows multifurcating trees as user trees. + + "W" : Write option. + Using this option, the program will produce more information + than it dose for standard output. + + "B" : Bootstrap option. + This option gives the approximate bootstrap probabilities of + candidate trees by a resampling of estimated likelihood (RELL) + method (Kishino et al., 1990). + + + Format of input data file + + We have tried to adhere to a rather stereotyped input format +similar to that of Felsenstein's programs. The simplest version +of the input file looks something like this: + + 4 40 W + species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV + species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV + species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV + species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV + + The first line of the input file contains the number of +species and the length of amino acid sequences, in free format, +separated by blanks. The information for each species follows, +starting with a ten-character species name (which can include +punctuation marks), and continuing with the characters for that +species. + + An input file has three parts of data; i.e., arguments, +sequences and topologies. + + 1. Arguments + The first line of the file gives number of species, sequence + length, and options. + + 2. Sequences + The following lines give species names and amino acid sequence + data. The amino acids must be specified by the one letter + codes adopted by IUPAC-IUB Commission on Biochemical + Nomenclature (1968). The amino acid code must be one of the + twenty. + + 3. Topologies + If one specifies User or Semi-automatic options, one mast + specify the number of topologies followed by the topologies + themselves. + + This program allows the option U, which signals that user- +defined tree(s) are provided. The topologies of these trees are +supplied AFTER the species and sequence data, rather than before +them. The letter U appears on the first line of the file. After +the species and sequence data, a line containing the number of +user-defined trees appears. Each user-defined tree starts on a +new line. Here is an example with three user-defined trees: + + 5 40 U B + species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV + species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV + species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV + species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV + species5 AINDCSCGHHLWMFPSLCYVRRNECQGGHIWKMFPLTVCA + 3 + (((species1,species2),species3),species4,species5) + ((species1,species2),(species3,species4),species5) + (species1,(species2,species3),(species4,species5)) + + An example of semi-auto mode is as follows: + + 5 40 S + species1 ARNDCQEGHILKAFPMTWYVARNDCQEGHISKMFGWTWYV + species2 ARNHNQCGHILKMFPMTSYVARNCCAEHHILKHFPSTWIV + species3 AINDCQEGHHLKMFPMTMYSVRNRIQEMHIQKHCPHTHYV + species4 AINHCQCEHILWMFPSTPYVARNDIQNYHILKMPPSTWWV + species5 AINDCSCGHHLWMFPSLCYVRRNECQGGHIWKMFPLTVCA + + ((species1,species2,species3),species4,species5) + + The tree topology is specified by nested pairs of +parentheses, enclosing species names and separated by commas. +Trailing blanks in the name may be omitted. The pattern of the +parentheses indicates the pattern of the tree by having each pair +of parentheses enclose all the members of a monophyletic group. +The entire tree is enclosed in an outermost pair of parentheses. +Note that the tree is an unrooted one, and therefore its base +must be multifurcation with a multiplicity of greater than or +equal to three. A specification of a tree ends with a semicolon +which may be omitted. + + + Program Constants + + The CONSTants in program that may be changed by a user are: + + CONST + maxsp : maximum number of species + maxnode : maxsp * 2 - 3 + maxpair : maxsp * (maxsp-1) / 2 + maxsite : maximum number of sites + maxptrn : maximum number of different site patterns + maxtree : maximum number of user trees + maxsmooth : number of smoothing algorithm + maxiterat : number of iterates of Newton method + epsilon : stopping value of error + minarc : lower limit on number of substitutions per branch + maxarc : upper limit on number of substitutions per branch + prprtn : proprtion of branch length + maxboot : number of bootstrap replications + maxexe : number of jobs + maxline : length of sequence output per line + maxname : maximum number of characters in species name + maxami : number of amino acids + minreal : if job is in underflow error, increase this value + seqfname : input file of sequence data + tpmfname : input file of transition probability + lklfname : output file of log-likelihood + + + Output Format + + The output usually consists of + (1) the name of the program and its version number, + (2) the input information printed out, and + (3) a series of trees, +some with associated information indicating how much change there +was in each character or on each part of the tree. + + The tree grows from left to right and has branches that are +approximately proportional in length to the lengths that the +program estimates. In some cases when branches are estimated to +be very short, the output makes them three spaces long so that +the topology is clearly shown. Here is what a typical tree looks +like: + + :-----------1.Tabac.chl + 0: + : :-------2.Prochloro + : :----6 + : : :---3.Anacystis + :---7 + : :------------------5.Synechocy + : + :------4.Fremyella + + No. number Length S.E. + ---------------------------------------------- + Tabac.chl 1 9.44861 ( 1.63423 ) + Prochloro 2 5.69634 ( 1.30862 ) + Anacystis 3 1.57704 ( 0.74325 ) + Fremyella 4 4.92061 ( 1.24297 ) + Synechocy 5 16.05818 ( 2.24639 ) + 6 2.13260 ( 0.86082 ) + 7 1.01070 ( 0.63908 ) + ---------------------------------------------- + ln L : -1813.614 ( 66.205 ) AIC : 3641.229 + ---------------------------------------------- + + Length refers to the estimated number of substitutions per +100 amino acid sites along the branch leading to the node (or +leaf) indicated by the number, and S.E. refers to its standard +error estimated by the formula of Kishino and Hasegawa (1989). + + + + Installing PROTML and Executive Environment + + + Personal computer with MS-DOS + Turbo Pascal(Borland): e.g. +IBM PCs and compatibles, NEC PC-98x. Please remove or change +comments marked as shown below: + + (* TURBO Pascal *) + + UNIX Workstation + standard Pascal compiler: e.g. SUN. +Please remove or change comments marked as shown below: + + (* SUN Pascal *) + + Mainframe computer (IBM and compatibles) + standard Pascal +compiler. For example, JCL (Job Control Language) of batch job. + + //USERIDB JOB PATHWORD + //STEP EXEC OPASCLG + //PASC.SYSIN DD DSN='USERID.PROTML.PASCAL',DISP=SHR + //GO.SEQFILE DD DSN='USERID.SEQFILE.DATA',DISP=SHR + + + + How to contact developers + + + The best way to contact developers is to send an E-mail. + + E-mail: adachi@ism.ac.jp + +If you prefer, write a letter with your comments and send it to + + Jun Adachi + Department of Statistical Science, + The Graduate University for Advanced Study, + 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan + FAX: +81-3-3446-1695 + + Please send a mail with the following information + + 1. Computer brand, model. + 2. The brand and version number of Pascal compiler. + 3. Operating system and version number. + 4. The input file of sequence data. + 5. The output file. + + + + Acknowledgements + + + We are particularly grateful to Dr. H. Kishino for +invaluable advices during the course of this work, and to Dr. J. +Felsenstein for generously permitting us to use routines in +DNAML. We also thank Drs. T. Hashimoto, T. Miyata and T. Yano for +discussions and comments. This work was carried out under the +Institute of Statistical Mathematics Cooperative Research Program +(90-ISM-57, 91-ISM-69), and was supported by grants from the +Ministry of Education, Science, and Culture of Japan. + + + + References + + +Adachi, J., Hasegawa, M. (1992) + Amino acid substitution of proteins coded for in mitochondrial +DNA during mammalian evolution. Jpn. J. Genet., 67:187-197. + +Adachi, J., Cao, Y., Hasegawa, M. (1993) + Tempo and mode of mitochondrial DNA evolution in vertebrates at +the amino acid sequence level: rapid evolution in warm-blooded +vertebrates. J. Mol. Evol., 36:270-281. + +Adkins, R.M., Honeycutt, R.L. (1991) + Molecular phylogeny of the superorder Archonta. Proc. Natl. +Acad. Sci. US., 88:10317-10321. + +Akaike, H. (1974) + A new look at the statistical model identification. IEEE Trans. +Autom. Contr., 19:716-723. + +Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) + A model of evolutionary change in proteins. In: Dayhoff, M.O. +(ed.) Atlas of Protein Sequence Structur., Vol~5, Suppl~3. +National Biomedical Research Foundation, Washington DC, pp.~345- +352. + +Disotell, T.R., Honeycutt, R.L., Ruvolo, M. (1992) + Mitochondrial DNA phylogeny of the Old-World monkey tribe +Papionini. Mol. Biol. Evol., 9:1-13. + +Doebley, J., Durbin, M., Golenberg, E.M., Clegg, M.T., Ma D.-P. +(1990) + Evolutionary analysis of the large subunit of carboxylase ( rbc +L) nucleotide sequence among the grasses (Gramineae). Evolutio., +44:1097-1108. + +Edwards, S.V., Arctander, P., Wilson, A.C. (1991) + Mitochondrial resolution of a deep branch in the genealogical +tree for perching birds. Proc. Roy. Soc. Londo., B243:99-107. + +Felsenstein. J. (1978a) + The number of evolutionary trees. System. Zool., 27:27-33. + +Felsenstein. J. (1978b) + Cases in which parsimony and compatibility methods will be +positively misleading. System. Zool., 27:401-410 + +Felsenstein, J. (1981) + Evolutionary trees from DNA sequences: a maximum likelihood +approach. J. Mol. Evol., 17:368-376 + +Felsenstein, J. (1985) + Confidence limits on phylogenies: an approach using the +bootstrap. Evolutio., 39:783-791. + +Felsenstein, J. (1992) + Phylogenies from restriction sites: a maximum-likelihood +approach. Evolutio., 46:159-173. + +Golenberg, E.M., Giannasi, D.E., Clegg, M.T., Smiley, C.J., +Durbin, M., Henderson, D., Zurawski, G. (1990) + Chlorolplast DNA sequence from a Miocene Magnolia species. +Natur., 344:656-658. + +Hasegawa, M., Yano, T. (1984a) + Phylogeny and classification of Hominoidea as inferred from DNA +sequence data. Proc. Japan Acad., B60:389-392. + +Hasegawa, M., Yano, T. (1984b) + Maximum likelihood method of phylogenetic inference from DNA +sequence data. Bull. Biomet. Soc. Jp., 5:1-7. + +Hasegawa, M., Iida, Y., Yano, T., Takaiwa, F., Iwabuchi, M. +(1985) + Phylogenetic relationships among eukaryotic kingdoms inferred +from ribosomal RNA sequences. J. Mol. Evol., 22:32-38. + +Hasegawa, M., Kishino, H. (1989) + Confidence limits on the maximum-likelihood estimate of the +hominoid tree from mitochondrial- DNA sequences. Evolutio., +43:672-677. + +Hasegawa, M. (1990) + Phylogeny and molecular evolution in primates. Jpn. J. Genet., +65:243-265. + +Hasegawa, M. (1991) + Molecular phylogeny and man's place in Hominoidea. J. Anthrop. +Soc. Nippo., 99:49-61. + +Hasegawa, M., Kishino, H., Hayasaka, K., Horai, S. (1990a) + Mitochondrial DNA evolution in primates: Transition rate has +been extremely low in lemur. J. Mol. Evol., 31:113-121. + +Hasegawa, M., Iwabe, N., Mukohata, Y., Miyata, T. (1990b) + Close evolutionary relatedness of archaebacteria, Methanococcus +and Halobacteriu., to eukaryotes demonstrated by composite +phylogenetic trees of elongation factors EF-Tu and EF-G: eocyte +tree is unlikely. Jpn. J. Genet., 65:109-114. + +Hasegawa, M., Kishino, H., Saitou, N. (1991) + On the maximum likelihood method in molecular phylogenetics. J. +Mol. Evol., 32:443-445. + +Hasegawa, M., Cao, Y., Adachi, J., Yano, T. (1992) + Rodent polyphyly? Natur., 355:595-595. + +Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N., Miyata, T. +(1993) + Early divergences in the evolution of eukaryotes: ancient +divergence of Entamoeba that lacks mitochondria revealed by +protein sequence data. J. Mol. Evol., 36:380-388. + +Hashimoto, T., Otaka, E., Adachi, J., Mizuta, K., Hasegawa, M. +(1993) + The giant panda is most close to a bear, judged by - and +-hemoglobin sequences. J Mol Evol. 36:282-289. + +IUPAC-IUB Commission on Biochemical Nomenclature (1968) + A one-letter notation for amino acid sequences, tentative rules. +J. Biol. Chem., 243:3557-3559. + + +Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S., Miyata, T. (1989) + Evolutionary relationship of archaebacteria, eubacteria, and +eukaryotes inferred from phylogenetic trees of duplicated genes. +Proc. Natl. Acad. Sci. US., 86:9355-9359. + +Iwabe, N., Kuma, K., Kishino, H., Hasegawa, M., Miyata, T. (1991) + Evolution of RNA polymerases and branching patterns of the three +major groups of archaebacteria. J. Mol. Evol., 32:70-78. + +Kishino, H., Hasegawa, M. (1989) + Evaluation of the maximum likelihood estimate of the +evolutionary tree topologies from DNA sequence data, and the +branching order in Hominoidea. J. Mol. Evol., 29:170-179. + +Kishino, H., Miyata, T., Hasegawa, M. (1990) + Maximum likelihood inference of protein phylogeny and the origin +of chloroplasts. J. Mol. Evol., 30:151-160. + +Les, D.H., Garvin, D.K., Wimpee, C.F. (1991) + Molecular evolutionary history of ancient aquatic angiosperms. +Proc. Natl. Acad. Sci. US., 88:10119-10123. + +Lockhart, P.J., Howe, C.J., Bryant, D.A., Beanland, T.J., Larkum, +A.W.D. (1992) + Substitutional bias confounds inference of cyanelle origins from +sequence data. J. Mol. Evol., 34:153-162. + +Loomis, W.F., Smith, D.W. (1990) + Molecular phylogeny of Dictyostelium discoideum by protein +sequence comparison. Proc. Natl. Acad. Sci. US., 87:9093-9097. + +Miyata, T., Iwabe, N., Kuma, K., Kawanishi, Y., Hasegawa, M., +Kishino, H., Mukohata, Y., Ihara, K., Osawa, S. (1991) + Evolution of archaebacteria: Phylogenetic relationships among +archaebacteria, eubacteria, and eukaryotes. In: Osawa, S., Honjo, +T. (eds.) Evolution of Life: Fossils, Molecules, and Culture . +Springer-Verlag, Tokyo, pp. 337-351. + +Mukohata, Y., Ihara, K., Kishino, H., Hasegawa, M., Iwabe, N., +Miyata, T. (1990) + Close evolutionary relatedness of archaebacteria with +eukaryotes. Proc. Japan Acad., B66:63-67. + +Saitou, N, Nei, M. (1987) + The neighbor-joining method: a new method for reconstructing +phylogenetic trees. Mol. Biol. Evol., 4:406-425. + +Ruvolo, M., Disotell, T.R., Allard, M.W., Brown, W.M., Honeycutt, +R.L. (1991) + Resolution of the African hominoid trichotomy by use of a +mitochondrial gene sequence. Proc. Natl. Acad. Sci. US., +88:1570-1574. + +Sogin, M.L., Edman, U., Elwood, H. (1989) + A single kingdom of eukaryotes. + In: Fernholm, B., Bremer, K., J rnvall, H. (eds.) The Hierarchy +of Life . Elsevier Science Publisher, Amsterdam, pp. 133-143. + +Woese, C.R. (1989) + Bacterial evolution. Microbiol. Rev., 51:221-271. + +Zillig, W., Klenk, H.-P., Palm, P., Leffers, H., P hler, G., +Gropp, F., Garrett, R.A. (1989) + Did eukaryotes originate by a fusion event? Endocytobiosis Cell +Res., 6:1-25 --- molphy-2.3b3.orig/debian/README +++ molphy-2.3b3/debian/README @@ -0,0 +1,38 @@ +MOLPHY: A Computer Program Package for Molecular Phylogenetics + +Readme + This is the MOLPHY (ProtML) distribution, version 2.3. + Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa. + All rights reserved. + + MOLPHY is a program package for MOLecular PHYlogenetics. + +ProtML is a main program in MOLPHY for inferring evolutionary trees from +PROTein (amino acid) sequences by using the Maximum Likelihood method. + +Programs (C language) + ProtML: Maximum Likelihood Inference of Protein Phylogeny + NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny + ProtST: Basic Statistics of Protein Sequences + NucST: Basic Statistics of Nucleic Acid Sequences + NJdist: Neighbor Joining Phylogeny from Distance Matrix +Utilities (Perl) + mollist: get identifiers list molrev: reverse DNA sequences + molcat: concatenate sequences molcut: get partial sequences + molmerge: merge sequences nuc2ptn: DNA -> Amino acid + rminsdel: remove INS/DEL sites molcodon: get specified codon sites + molinfo: get varied sites mol2mol: MOLPHY format beautifer + inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved + mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY + must2mol: MUST -> MOLPHY etc. + +MOLPHY is a free software, and you can use and redistribute it. +The programs are written in a standard subset of C with UNIX-like OS. +The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS. +MOLPHY has been tested on SUN4's (cc & gcc with SUN-OS 4.1.3) and +HP9000/700 (cc, c89 & gcc with HP-UX 9.05). +However, MOLPHY has NOT been tested on VAX, IBM-PC, and Macintosh. + +NETWORK DISTRIBUTION ONLY: The latest version of MOLPHY is always available +by anonymous ftp in sunmh.ism.ac.jp(133.58.12.20): /pub/molphy* +or in ftp.ism.ac.jp: /pub/ISMLIB/MOLPHY/. --- molphy-2.3b3.orig/debian/README.Debian +++ molphy-2.3b3/debian/README.Debian @@ -0,0 +1,62 @@ +molphy for DEBIAN +----------------- + +Because there are no upstream changes since 5 years I consider the +project to be dead. Anyway it is used in Arb which I want to package +I build this package separately. Thus I also applied all patches +from Arb. + +Molphy uses a strange source philosophy. In the original Makefile +some source files are forced to be a copy of some others. The +different targets are just built by different defines. Because I +had to modify the source package (it was not gzipped) I decided to +use symlinks instead of the identical copies to represent this fact +and to make it easier to keep patches in sync. + +Thos files are: + Source Link (*) means there was a patch in Arb + (???) Missing in source + distan.c Ndistan.c + dmlproc.c Ndmlproc.c (???) + mlklhd.c Nmlklhd.c + protdml.c Nucdml.c (???) + protml.c Nucml.c Nuctpm.c Prottpm.c (*) + protst.c Nucst.c + pstree.c Dpstree.c (*) + seqstat.c Nseqstat.c + tpmproc.c Ntpmproc.c (???) + tranprb.c Ntranprb.c Ntrnprbt.c Trnprbt.c + tridist.c Njdist.c + +Strangely enough there is a RMSRC rule in the Makefile which might have +deleted the sources marked with (???). There is no rule to rebuild those +files ... +I removed at least those filenames from the RMSRC rule which obviousely +are needed to build some targets to avoid an accident. + +The Arb patches include a header file prot_tml.h which was created using +a tool named mkptypes with the following description: + + Program to extract function declarations from C source code + Written by Eric R. Smith and placed in the public domain + Thanks to: + Jwahar R. Bammi, for catching several bugs and providing the Unix makefiles + Byron T. Jenings Jr. for cleaning up the space code, providing a Unix + manual page, and some ANSI and C++ improvements. + Skip Gilbrech for code to skip parameter names in prototypes. + ... and many others for helpful comments and suggestions. + Patchlevel 1: Feb. 16, 1991 + +The package is shipped with a documentation of the old version 1. +Well - better old documentation than non documentation. I found it on + http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/PROTMLver1.DOC +Please write an e-mail if you know about any more recent documentation. + +The same URL has some Examples. Those examples had some result files +which are built with an older version (2.2) than this one (2.3b3) which +differ more or less from the results of this package. I ship those +results which are more different than some floats which differ below 1%. +Please read /usr/share/doc/molphy/examples/tests/compare/README.compare +for further explanation. There is a makefile to test the examples. + +Andreas Tille Mon, 29 Oct 2001 22:34:09 +0100 --- molphy-2.3b3.orig/debian/changelog +++ molphy-2.3b3/debian/changelog @@ -0,0 +1,32 @@ +molphy (2.3b3-3) unstable; urgency=low + + * Standards-Version: 3.7.2 (no changes needed) + * Switched to cdbs + * Added DebTags + + -- Andreas Tille Sun, 10 Sep 2006 15:44:10 +0200 + +molphy (2.3b3-2) unstable; urgency=low + + * Rebuild to remove /usr/doc link + * Standards-Version: 3.6.2.1 + * debian/compat + * Mention new home page in debian/{copyright,control} + * debhelper (>= 4) + * Use -O3 instead of -O2 + + -- Andreas Tille Sat, 13 Aug 2005 11:22:43 +0200 + +molphy (2.3b3-1) unstable; urgency=low + + * Initial Release. + closes: #118355 + * Rebuild source tarball because it was not gzipped. Used symlinks + instead of copies from some source files. + * Applied Arb patches. + * Wrote manpages + * Added documentation of older version because MolPhy comes without + any documentation + * Added examples and makefile to test them. + + -- Andreas Tille Mon, 12 Nov 2001 10:56:06 +0100 --- molphy-2.3b3.orig/debian/compat +++ molphy-2.3b3/debian/compat @@ -0,0 +1 @@ +5 --- molphy-2.3b3.orig/debian/control +++ molphy-2.3b3/debian/control @@ -0,0 +1,31 @@ +Source: molphy +Section: non-free/science +Priority: optional +Maintainer: Andreas Tille +Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5) +Standards-Version: 3.7.2 + +Package: molphy +Architecture: any +Depends: ${shlibs:Depends}, ${perl:Depends} +Suggests: phylip +Description: [Biology] Program Package for MOLecular PHYlogenetics + ProtML is a main program in MOLPHY for inferring evolutionary trees from + PROTein (amino acid) sequences by using the Maximum Likelihood method. + Other programs (C language) + NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny + ProtST: Basic Statistics of Protein Sequences + NucST: Basic Statistics of Nucleic Acid Sequences + NJdist: Neighbor Joining Phylogeny from Distance Matrix + Utilities (Perl) + mollist: get identifiers list molrev: reverse DNA sequences + molcat: concatenate sequences molcut: get partial sequences + molmerge: merge sequences nuc2ptn: DNA -> Amino acid + rminsdel: remove INS/DEL sites molcodon: get specified codon sites + molinfo: get varied sites mol2mol: MOLPHY format beautifer + inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved + mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY + must2mol: MUST -> MOLPHY etc. + . + Homepage: http://www.ism.ac.jp/ismlib/softother.e.html +XB-Tag: suite::debian-med:bio, legacy::science, made-of::lang:c, made-of::lang:perl --- molphy-2.3b3.orig/debian/control.in +++ molphy-2.3b3/debian/control.in @@ -0,0 +1,31 @@ +Source: molphy +Section: non-free/science +Priority: optional +Maintainer: Andreas Tille +Build-Depends: @cdbs@ +Standards-Version: 3.7.2 + +Package: molphy +Architecture: any +Depends: ${shlibs:Depends}, ${perl:Depends} +Suggests: phylip +Description: [Biology] Program Package for MOLecular PHYlogenetics + ProtML is a main program in MOLPHY for inferring evolutionary trees from + PROTein (amino acid) sequences by using the Maximum Likelihood method. + Other programs (C language) + NucML: Maximum Likelihood Inference of Nucleic Acid Phylogeny + ProtST: Basic Statistics of Protein Sequences + NucST: Basic Statistics of Nucleic Acid Sequences + NJdist: Neighbor Joining Phylogeny from Distance Matrix + Utilities (Perl) + mollist: get identifiers list molrev: reverse DNA sequences + molcat: concatenate sequences molcut: get partial sequences + molmerge: merge sequences nuc2ptn: DNA -> Amino acid + rminsdel: remove INS/DEL sites molcodon: get specified codon sites + molinfo: get varied sites mol2mol: MOLPHY format beautifer + inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved + mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY + must2mol: MUST -> MOLPHY etc. + . + Homepage: http://www.ism.ac.jp/ismlib/softother.e.html +XB-Tag: suite::debian-med:bio, legacy::science, made-of::lang:c, made-of::lang:perl --- molphy-2.3b3.orig/debian/copyright +++ molphy-2.3b3/debian/copyright @@ -0,0 +1,23 @@ +This package was debianized by Andreas Tille +Mon, 5 Nov 2001 23:50:39 +0100 + +Homepage: + http://www.ism.ac.jp/ismlib/softother.e.html + +It was downloaded by anonymous ftp from: + ftp://ftp.ism.ac.jp/pub/ISMLIB/MOLPHY/molphy-2.3b3.tar.Z + +The examples and the documentation was found on + http://bioweb.pasteur.fr/docs/doc-gensoft/molphy/ + +Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa. +All rights reserved. + +License: + +MOLPHY is a free software, and you can use and redistribute it. + +I wrote an e-mail to the authors if they could fix this license because +it conflicts with DFSG #3 (Derived works) but I got no response yet. +So I just put the package under non-free and I´m hoping that someone +will respond the next couple of weeks. --- molphy-2.3b3.orig/debian/dirs +++ molphy-2.3b3/debian/dirs @@ -0,0 +1 @@ +usr/bin --- molphy-2.3b3.orig/debian/docs +++ molphy-2.3b3/debian/docs @@ -0,0 +1,3 @@ +debian/FORMAT +debian/PROTMLver1.DOC +debian/README --- molphy-2.3b3.orig/debian/examples +++ molphy-2.3b3/debian/examples @@ -0,0 +1 @@ +debian/tests --- molphy-2.3b3.orig/debian/install +++ molphy-2.3b3/debian/install @@ -0,0 +1,6 @@ +src/protml usr/bin +src/protst usr/bin +src/nucml usr/bin +src/nucst usr/bin +src/njdist usr/bin +src/totalml usr/bin --- molphy-2.3b3.orig/debian/links +++ molphy-2.3b3/debian/links @@ -0,0 +1,47 @@ +usr/share/man/man1/protml.1 usr/share/man/man1/njdist.1 +usr/share/man/man1/protml.1 usr/share/man/man1/nucml.1 +usr/share/man/man1/protml.1 usr/share/man/man1/nucst.1 +usr/share/man/man1/protml.1 usr/share/man/man1/protst.1 +usr/share/man/man1/protml.1 usr/share/man/man1/totalml.1 + +usr/share/man/man1/mollist.1 usr/share/man/man1/ali2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/clus2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/degene4l.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/degene4.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/disjoint.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/dna2ami.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/eali2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/egetcds.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/getcds.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/ggetcds.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/inf2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/infocode2.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/infocode.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/int2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mc2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mega2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mol2inf.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mol2int.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mol2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mol2phy.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/mol2seq.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molcat.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molcodon.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molcons.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molcut.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molinfo.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molmerge.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molrev.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/molsplit.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/must2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/njt2tpl.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2code.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2NUC.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/nuc2ptn.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/phy2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/rmid3.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/rminsdel.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/rmleu.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/rmsyno.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/seq2mol.1 +usr/share/man/man1/mollist.1 usr/share/man/man1/seqwrap.1 --- molphy-2.3b3.orig/debian/manpages +++ molphy-2.3b3/debian/manpages @@ -0,0 +1,2 @@ +debian/mollist.1 +debian/protml.1 --- molphy-2.3b3.orig/debian/mollist.1 +++ molphy-2.3b3/debian/mollist.1 @@ -0,0 +1,215 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH "MolPhy Utilities" 1 "November 7, 2001" "MOLecular PHYlogenetics" +.SH NAME +.B MolPhy Utilities +\- program package for MOLecular PHYlogenetics + +The Molphy package includes several Perl utilities: + +.B mollist +\- get identifiers list +.br +.B molrev +\- reverse DNA sequences +.br +.B molcat +\- concatenate sequences +.br +.B molcut +\- get partial sequences +.br +.B molmerge +\- merge sequences +.br +.B nuc2ptn +\- DNA -> Amino acid +.br +.B rminsdel +\- remove INS/DEL sites +.br +.B molcodon +\- get specified codon sites +.br +.B molinfo +\- get varied sites +.br +.B mol2mol +\- MOLPHY format beautifer +.br +.B int2mol +\- Interleaved -> MOLPHY +.br +.B mol2int +\- MOLPHY -> Interleaved +.br +.B mol2phy +\- MOLPHY -> Sequential +.br +.B phy2mol +\- Sequential -> MOLPHY +.br +.B must2mol +\- MUST -> MOLPHY +.br +many more perl conversion utilities which are not further described + +.SH SYNOPSIS +.B mollist +.RB [sequence_file] +.br +.B molrev +.RB [sequence_file] +.br +.B molcat +.RB [sequence_file] +.br +.B molcut +.RB [sequence_file] +.br +.B molmerge +.RB [sequence_file] +.br +.B nuc2ptn +.RB [switches] +.RB [sequence_file] +.br +.B rminsdel +.RB [switches] +.RB [sequence_file] +.br +.B molcodon +.RB [sequence_file] +.br +.B molinfo +.RB [switches] +.RB [sequence_file] +.br +.B mol2mol +.RB [sequence_file] +.br +.B inl2mol +.RB [sequence_file] +.br +.B mol2int +.RB [sequence_file] +.br +.B mol2phy +.RB [sequence_file] +.br +.B phy2mol +.RB [sequence_file] +.br +.B must2mol +.RB [sequence_file] +.br +.B ali2mol +.RB [sequence_file] +.br +.B clus2mol +.RB [sequence_file] +.br +.B degene4l +.RB [switches] +.RB [sequence_file] +.br +.B degene4 +.RB [switches] +.RB [sequence_file] +.br +.B disjoint +.RB [sequence_file] +.br +.B dna2ami +.RB [options] +.RB [no_align_files] +.br +.B eali2mol +.RB [EMBL_ALIGN_file] +.br +.B egetcds +.RB [EMBL_file] +.br +.B getcds +.RB [EMBL_file] +.br +.B egetcds +.RB [Genbank_file] +.br +.B info2mol +.RB [sequence_file] +.br +.B infocode +.RB [switches] +.RB [sequence_file] +.br +.B infocode +.RB [switches] +.RB [sequence_file] +.br +.B mc2mol +.RB [sequence_file] +.br +.B mega2mol +.RB [sequence_file] +.br +.B mol2info +.RB [sequence_file] +.br +.B mol2seq +.RB [sequence_file] +.br +.B molcons +.RB [sequence_file] +.br +.B molsplit +.RB [sequence_file] +.br +.B njt2tpl +.RB [machine_readable_tree_with_branch_length] +.br +.B mol2mol +.RB [sequence_file] +.br +.B nuc2NUC +.RB [sequence_file] +.br +.B rmid3 +.RB [switches] +.RB [sequence_file] +.br +.B rmleu +.RB [switches] +.RB [sequence_file] +.br +.B rmsyno +.RB [switches] +.RB [sequence_file] +.br +.B seq2mol +.RB [sequence_file] +.br +.B seqwrap +.RB [file] + +.SH DESCRIPTION +This is the Debian GNU/Linux version of the +MOLPHY (ProtML) distribution, version 2.3. +Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa. +All rights reserved. + +MOLPHY is a program package for MOLecular PHYlogenetics. + +The perl utilities above are usefull to convert different formats +of phylogenetic data. + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- molphy-2.3b3.orig/debian/protml.1 +++ molphy-2.3b3/debian/protml.1 @@ -0,0 +1,79 @@ +'\" t +.\" ** The above line should force tbl to be a preprocessor ** +.\" Copyright (C), 2001, Andreas Tille +.\" +.\" You may distribute under the terms of the GNU General Public +.\" License as specified in the file COPYING that comes with the +.\" man_db distribution. +.\" +.\" +.TH MolPhy 1 "November 7, 2001" "MOLecular PHYlogenetics" +.SH NAME +.B MolPhy +\- program package for MOLecular PHYlogenetics + +Molphy consists of several programs: + +.B protml +\- Maximum Likelihood Inference of Protein Phylogeny +.br +.B nucml +\- Maximum Likelihood Inference of Nucleic Acid Phylogeny +.br +.B protst +\- Basic Statistics of Protein Sequences +.br +.B nucst +\- Basic Statistics of Nucleic Acid Sequence +.br +.B njdist +\- Neighbor Joining Phylogeny from Distance Matrix +.br +.B totalml +\- Total ML Inference of Molecular Phylogeny + +.SH SYNOPSIS +.B protml +.RB [switches] +.IR sequence_file +.IR [topology_file] +.br +.B nucml +.RB [switches] +.IR sequence_file +.IR [topology_file] +.br +.B protst +.RB [switches] +.IR sequence_file +.br +.B nucst +.RB [switches] +.IR sequence_file +.br +.B njdist +.RB [switches] +.IR distance_matrix_file +.br +.B totalml +.RB [switches] +.IR LLS_files + +.SH DESCRIPTION +This is the Debian GNU/Linux version of the +MOLPHY (ProtML) distribution, version 2.3. +Copyright (c) 1992-1996, Jun Adachi & Masami Hasegawa. +All rights reserved. + +MOLPHY is a program package for MOLecular PHYlogenetics. + +ProtML is a main program in MOLPHY for inferring evolutionary trees from +PROTein (amino acid) sequences by using the Maximum Likelihood method. + +Each single program has a +.B -h +switch which shows some help. + +.SH AUTHOR +This manual page was written by Andreas Tille , +for the Debian GNU/Linux system (but may be used by others). --- molphy-2.3b3.orig/debian/rules +++ molphy-2.3b3/debian/rules @@ -0,0 +1,29 @@ +#!/usr/bin/make -f +# debian/rules for molphy using cdbs +# Andreas Tille , GPL + +pkg=molphy + +DEB_AUTO_UPDATE_DEBIAN_CONTROL := yes + +include /usr/share/cdbs/1/rules/simple-patchsys.mk +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/class/makefile.mk + +clean:: + cd src; make clean + +# Use makefile in subdir +# Remark: mentioning INSTALLDIR does not have any effect because the +# install target is not called by cdbs by default; just lets use debian/install +# DEB_MAKE_INVOKE = cd src; $(DEB_MAKE_ENVVARS) make INSTALLDIR=../debian/$(pkg)/usr/bin $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)") +DEB_MAKE_INVOKE = cd src; $(DEB_MAKE_ENVVARS) make $(if $(DEB_MAKE_MAKEFILE), -f $(DEB_MAKE_MAKEFILE),) -C $(DEB_BUILDDIR) CFLAGS=$(if $(CFLAGS_$(cdbs_curpkg)),"$(CFLAGS_$(cdbs_curpkg))","$(CFLAGS)") CXXFLAGS=$(if $(CXXFLAGS_$(cdbs_curpkg)),"$(CXXFLAGS_$(cdbs_curpkg))","$(CXXFLAGS)") + +install/molphy:: + ### replace perl path from /usr/local/bin to /usr/bin which is + ### in principle what utl/Install is doing + # for utl in `ls utl/*.pl` ; do \ + # sed 's?#!/usr/local/bin/perl?#!/usr/bin/perl?' $${utl} > `pwd`/debian/`dh_listpackages`/usr/bin/`basename $${utl} .pl` ; \ + # done + ### But why not using the original script ?? + cd utl; ./Install ../debian/$(pkg)/usr/bin