--- glam2-1064.orig/debian/glam2-purge.1
+++ glam2-1064/debian/glam2-purge.1
@@ -0,0 +1,92 @@
+.\" Title: GLAM2-PURGE
+.\" Author: Andrew Neuwald
+.\" Generator: DocBook XSL Stylesheets v1.73.2
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2\-PURGE" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2-purge \- Removes redundant sequences from a FASTA file
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR]
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2\-purge\fR
+is a modified version of Andrew Neuwald\'s
+\fBpurge\fR
+program that removes redundant sequences from a FASTA file\&. This is recommended in order to prevent highly similar sequences distorting the search for motifs\&. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user\&. The output file is named \&.\&. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/\-1 scoring scheme for DNA\&. Purge can also be used to mask tandem repeats\&. It uses the XNU program for this purpose\&.
+.SH "OPTIONS"
+.PP
+\fB\-n\fR
+.RS 4
+Sequences are DNA (default: protein)\&.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Use blast heuristic method (default for protein)\&.
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+Use an exhaustive method (default for DNA)\&.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Keep first sequence in the set\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Use xnu to mask protein tandem repeats\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2\fR(1),
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2scan\fR(1),
+\fBxnu\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCES"
+.PP
+Purge was written by Andy Neuwald and is described in more detail in Neuwald et al\&., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618\(en1632, 1995\&. Please cite it if you use Purge\&.
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBAndrew Neuwald\fR
+.sp -1n
+.IP "" 4
+Author of purge, renamed glam2\-purge in Debian\&.
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of Purge and GLAM2 are released in the public domain\&.
+.sp
--- glam2-1064.orig/debian/glam2mask.1.xml
+++ glam2-1064/debian/glam2mask.1.xml
@@ -0,0 +1,131 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+ &dhtitle;
+
+ &dhproduct;
+ &dhrelease;
+
+
+ Martin
+ C
+ Frith
+ Author of GLAM2.
+
+
+ Timothy
+ L
+ Bailey
+ Author of GLAM2.
+
+
+ &dhfirstname;
+ &dhsurname;
+ Formatted this manpage in DocBook XML for the Debian distribution.
+
+ &dhemail;
+
+
+
+
+ The source code and the documentation of GLAM2 are released in the public domain.
+
+
+
+ &dhucpackage;
+ &dhsection;
+
+
+ &dhpackage;
+ masks a GLAM2 motif in sequences
+
+
+
+ &dhpackage;
+
+ my_motif.glam2
+ my_seqs.fa
+
+
+
+
+ DESCRIPTION
+
+ &dhpackage; masks a glam2 motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with the symbol 'x'. By alternately applying glam2 and glam2mask several times, it is possible to find the strongest, second-strongest, third-strongest, etc. motifs in a set of sequences.
+
+
+
+
+ OPTIONS (default settings)
+
+
+
+
+
+ Output file (stdout).
+
+
+
+
+
+
+ Mask character (x).
+
+
+
+
+
+
+ SEE ALSO
+
+
+ glam2format
+ 1
+ ,
+ glam2
+ 1
+ ,
+ glam2-purge
+ 1
+ ,
+ glam2scan
+ 1
+
+ The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.
+
+
+
+ REFERENCE
+
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+
+
+
--- glam2-1064.orig/debian/watch
+++ glam2-1064/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip
--- glam2-1064.orig/debian/glam2scan.1.xml
+++ glam2-1064/debian/glam2scan.1.xml
@@ -0,0 +1,182 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+ &dhtitle;
+
+ &dhproduct;
+ &dhrelease;
+
+
+ Martin
+ C
+ Frith
+ Author of GLAM2.
+
+
+ Timothy
+ L
+ Bailey
+ Author of GLAM2.
+
+
+ &dhfirstname;
+ &dhsurname;
+ Formatted this manpage in DocBook XML for the Debian distribution.
+
+ &dhemail;
+
+
+
+
+ The source code and the documentation of GLAM2 are released in the public domain.
+
+
+
+ &dhucpackage;
+ &dhsection;
+
+
+ &dhpackage;
+ finds a GLAM2 motif in a database
+
+
+
+ &dhpackage;
+
+
+ my_motif.glam2
+ my_seqs.fa
+
+ An alphabet other than p or n is interpreted as the name of an alphabet file.
+
+
+
+ DESCRIPTION
+
+ glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits the motif.
+
+
+
+
+ OPTIONS (default settings)
+
+
+
+
+
+ Show all options and their default settings.
+
+
+
+
+
+
+ Output file (stdout).
+
+
+
+
+
+
+ Number of alignments to report (25).
+
+
+
+
+
+
+ Examine both strands - forward and reverse complement.
+
+
+
+
+
+
+ Deletion pseudocount (0.1).
+
+
+
+
+
+
+ No-deletion pseudocount (2.0).
+
+
+
+
+
+
+ Insertion pseudocount (0.02).
+
+
+
+
+
+
+ No-insertion pseudocount (1.0).
+
+
+
+
+
+
+ Dirichlet mixture file.
+
+
+
+
+
+
+ SEE ALSO
+
+
+ glam2format
+ 1
+ ,
+ glam2mask
+ 1
+ ,
+ glam2-purge
+ 1
+ ,
+ glam2
+ 1
+
+ The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.
+
+
+
+ REFERENCE
+
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+
+
+
--- glam2-1064.orig/debian/docs
+++ glam2-1064/debian/docs
@@ -0,0 +1,4 @@
+README
+doc/*.html
+doc/*.css
+doc/*.pdf
--- glam2-1064.orig/debian/manpages
+++ glam2-1064/debian/manpages
@@ -0,0 +1,5 @@
+debian/glam2.1
+debian/glam2format.1
+debian/glam2mask.1
+debian/glam2-purge.1
+debian/glam2scan.1
--- glam2-1064.orig/debian/glam2mask.1
+++ glam2-1064/debian/glam2mask.1
@@ -0,0 +1,73 @@
+.\" Title: GLAM2MASK
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2MASK" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2mask \- masks a GLAM2 motif in sequences
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2mask\fR [\fBoptions\fR] \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2mask\fR
+masks a
+\fBglam2\fR
+motif out of sequences, so that weaker motifs can be found\&. Masking replaces residues aligned to key positions with the symbol \'x\'\&. By alternately applying
+\fBglam2\fR
+and
+\fBglam2mask\fR
+several times, it is possible to find the strongest, second\-strongest, third\-strongest, etc\&. motifs in a set of sequences\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Mask character (\fIx\fR)\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
--- glam2-1064.orig/debian/glam2.1.xml
+++ glam2-1064/debian/glam2.1.xml
@@ -0,0 +1,272 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+ &dhtitle;
+
+ &dhproduct;
+ &dhrelease;
+
+
+ Martin
+ C
+ Frith
+ Author of GLAM2.
+
+
+ Timothy
+ L
+ Bailey
+ Author of GLAM2.
+
+
+ &dhfirstname;
+ &dhsurname;
+ Formatted this manpage in DocBook XML for the Debian distribution.
+
+ &dhemail;
+
+
+
+
+ The source code and the documentation of GLAM2 are released in the public domain.
+
+
+
+ &dhucpackage;
+ &dhsection;
+
+
+ &dhpackage;
+ Gapped Local Alignment of Motifs
+
+
+
+ &dhpackage;
+
+
+ my_seqs.fa
+
+ An alphabet other than p or n is interpreted as the name of an alphabet file.
+
+
+
+ DESCRIPTION
+
+ GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.
+
+
+
+
+ OPTIONS (default settings)
+
+
+
+
+
+ Show all options and their default settings.
+
+
+
+
+
+
+ Output file (stdout).
+
+
+
+
+
+
+ Number of alignment runs (10).
+
+
+
+
+
+
+ End each run after this many iterations without improvement (10000).
+
+
+
+
+
+
+ Examine both strands - forward and reverse complement.
+
+
+
+
+
+
+ Minimum number of sequences in the alignment (2).
+
+
+
+
+
+
+ Minimum number of aligned columns (2).
+
+
+
+
+
+
+ Maximum number of aligned columns (50).
+
+
+
+
+
+
+ Initial number of aligned columns (20).
+
+
+
+
+
+
+ Dirichlet mixture file.
+
+
+
+
+
+
+ Deletion pseudocount (0.1).
+
+
+
+
+
+
+ No-deletion pseudocount (2.0).
+
+
+
+
+
+
+ Insertion pseudocount (0.02).
+
+
+
+
+
+
+ No-insertion pseudocount (1.0).
+
+
+
+
+
+
+ Weight for generic versus sequence-set-specific residue abundances (1e+99).
+
+
+
+
+
+
+ Initial temperature (1.2).
+
+
+
+
+
+
+ Cooling factor per n iterations (1.44).
+
+
+
+
+
+
+ Temperature lower bound (0.1).
+
+
+
+
+
+
+ Print progress information at each iteration.
+
+
+
+
+
+
+ Column-sampling moves per site-sampling move (1.0).
+
+
+
+
+
+
+ Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0).
+
+
+
+
+
+
+ Seed for pseudo-random numbers (1).
+
+
+
+
+
+
+ SEE ALSO
+
+
+ glam2format
+ 1
+ ,
+ glam2mask
+ 1
+ ,
+ glam2-purge
+ 1
+ ,
+ glam2scan
+ 1
+
+ The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.
+
+
+
+ REFERENCE
+
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+
+
+
--- glam2-1064.orig/debian/README.Debian
+++ glam2-1064/debian/README.Debian
@@ -0,0 +1,9 @@
+glam2 for Debian
+----------------
+
+We renamed purge glam2-purge, to avoid namespace collision.
+
+glam2 is compiled with -O2 optimisation level. Please contact us if you notice
+performance issues compared to -O3.
+
+ -- Steffen Moeller Tue, 13 Nov 2007 00:35:50 +0100
--- glam2-1064.orig/debian/glam2.doc-base.method
+++ glam2-1064/debian/glam2.doc-base.method
@@ -0,0 +1,9 @@
+Document: glam2-method
+Title: GLAM2 Methods
+Author: Martin C Frith
+Section: Science/Biology
+Abstract: This manual explains in detail
+ the statistical methods used in GLAM2.
+
+Format: PDF
+Files: /usr/share/doc/glam2/GLAM2_method.pdf
--- glam2-1064.orig/debian/rules
+++ glam2-1064/debian/rules
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+
+DEB_COMPRESS_EXCLUDE := .pdf # The PDF doc will not be compressed
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_MAKE_BUILD_TARGET = --directory src all glam2fft
+build/glam2::
+ $(DEB_MAKE_INVOKE) --directory purge
+
+BINDIR = $(CURDIR)/debian/glam2/usr/bin
+binary-fixup/glam2::
+ # purge is renamed glam2-purge to avoid namespace problems.
+ mv $(BINDIR)/purge $(BINDIR)/glam2-purge
+ # FFT is enabled by default in Debian.
+ mv $(BINDIR)/glam2fft $(BINDIR)/glam2
+
+clean::
+ rm -f purge/*.o purge/purge src/*.o src/glam2, src/glam2mask, scr/glam2format src/glam2scan src/glam2fft
+
+get-orig-source:
+ # The unzip command from the unzip package is needed for this one.
+ # Please update debian/changelog before calling this target.
+ [ -f ../glam2-$(DEB_UPSTREAM_VERSION).zip ] || uscan --force-download
+ unzip ../glam2-$(DEB_UPSTREAM_VERSION).zip -d..
+ tar --create --gzip --file ../glam2_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../glam2-$(DEB_UPSTREAM_VERSION)
--- glam2-1064.orig/debian/control
+++ glam2-1064/debian/control
@@ -0,0 +1,35 @@
+Source: glam2
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller , Charles Plessy
+Build-Depends: debhelper (>= 5), cdbs, quilt, libfftw3-dev
+Standards-Version: 3.7.3
+Homepage: http://bioinformatics.org.au/glam2/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/glam2/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/glam2/trunk/
+
+Package: glam2
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: gapped protein motifs from unaligned sequences
+ GLAM2 is a software package for finding motifs in sequences, typically
+ amino-acid or nucleotide sequences. A motif is a re-occurring sequence
+ pattern: typical examples are the TATA box and the CAAX prenylation motif. The
+ main innovation of GLAM2 is that it allows insertions and deletions in motifs.
+ .
+ The package includes these programs:
+ glam2: discovering motifs shared by a set of sequences;
+ glam2scan: finding matches, in a sequence database, to a motif discovered
+ by glam2;
+ glam2format: converting glam2 motifs to standard alignment formats;
+ glam2mask: masking glam2 motifs out of sequences, so that weaker motifs
+ can be found;
+ glam2-purge: removing highly similar members of a set of sequences.
+ .
+ In this package, the fast Fourier algorithm (FFT) was enabled for glam2.
+ .
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey
+ (2008) Discovering sequence motifs with arbitrary insertions and deletions,
+ PLoS Computational Biology (in press).
--- glam2-1064.orig/debian/glam2.1
+++ glam2-1064/debian/glam2.1
@@ -0,0 +1,174 @@
+.\" Title: GLAM2
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2 \- Gapped Local Alignment of Motifs
+.SH "SYNOPSIS"
+.HP 6
+\fBglam2\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\&.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\&.
+.SH "DESCRIPTION"
+.PP
+GLAM2 is a software package for finding motifs in sequences, typically amino\-acid or nucleotide sequences\&. A motif is a re\-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif\&. The main innovation of GLAM2 is that it allows insertions and deletions in motifs\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Number of alignment runs (\fI10\fR)\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+End each run after this many iterations without improvement (\fI10000\fR)\&.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\&.
+.RE
+.PP
+\fB\-z\fR
+.RS 4
+Minimum number of sequences in the alignment (\fI2\fR)\&.
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Minimum number of aligned columns (\fI2\fR)\&.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Maximum number of aligned columns (\fI50\fR)\&.
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Initial number of aligned columns (\fI20\fR)\&.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\&.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\&.02\fR)\&.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\&.
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+Initial temperature (\fI1\&.2\fR)\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Cooling factor per n iterations (\fI1\&.44\fR)\&.
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+Temperature lower bound (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Print progress information at each iteration\&.
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Column\-sampling moves per site\-sampling move (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Site sampling algorithm:
+\fI0\fR=FAST
+\fI1\fR=SLOW
+\fI2\fR=FFT (\fI0\fR)\&.
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Seed for pseudo\-random numbers (\fI1\fR)\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
--- glam2-1064.orig/debian/glam2scan.1
+++ glam2-1064/debian/glam2scan.1
@@ -0,0 +1,109 @@
+.\" Title: GLAM2SCAN
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2SCAN" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2scan \- finds a GLAM2 motif in a database
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2scan\fR [\fBoptions\fR] \fBalphabet\fR \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR
+.PP
+An alphabet other than
+\fIp\fR
+or
+\fIn\fR
+is interpreted as the name of an alphabet file\&.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2scan\fR
+finds matches, in a sequence database, to a motif discovered by
+\fBglam2\fR\&. Each match receives a score, indicating how well it fits the motif\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-h\fR
+.RS 4
+Show all options and their default settings\&.
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+Number of alignments to report (\fI25\fR)\&.
+.RE
+.PP
+\fB\-2\fR
+.RS 4
+Examine both strands \- forward and reverse complement\&.
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Deletion pseudocount (\fI0\&.1\fR)\&.
+.RE
+.PP
+\fB\-E\fR
+.RS 4
+No\-deletion pseudocount (\fI2\&.0\fR)\&.
+.RE
+.PP
+\fB\-I\fR
+.RS 4
+Insertion pseudocount (\fI0\&.02\fR)\&.
+.RE
+.PP
+\fB\-J\fR
+.RS 4
+No\-insertion pseudocount (\fI1\&.0\fR)\&.
+.RE
+.PP
+\fB\-d\fR
+.RS 4
+Dirichlet mixture file\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
--- glam2-1064.orig/debian/glam2-purge.1.xml
+++ glam2-1064/debian/glam2-purge.1.xml
@@ -0,0 +1,168 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+ &dhtitle;
+
+ &dhproduct;
+ &dhrelease;
+
+
+ Andrew
+ F
+ Neuwald
+ Author of purge, renamed glam2-purge in Debian.
+
+
+
+
+ Martin
+ C
+ Frith
+ Modified purge to be ANSI standard C and improved the user interface.
+
+
+ Timothy
+ L
+ Bailey
+ Modified purge to be ANSI standard C and improved the user interface.
+
+
+
+
+ &dhfirstname;
+ &dhsurname;
+ Formatted this manpage in DocBook XML for the Debian distribution.
+
+ &dhemail;
+
+
+
+
+ The source code and the documentation of Purge and GLAM2 are released in the public domain.
+
+
+
+ &dhucpackage;
+ &dhsection;
+
+
+ &dhpackage;
+ Removes redundant sequences from a FASTA file
+
+
+
+ &dhpackage;
+ file
+
+
+
+
+
+
+ DESCRIPTION
+
+ glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.
+
+
+
+
+ OPTIONS
+
+
+
+
+
+ Sequences are DNA (default: protein).
+
+
+
+
+
+
+ Use blast heuristic method (default for protein).
+
+
+
+
+
+
+ Use an exhaustive method (default for DNA).
+
+
+
+
+
+
+ Keep first sequence in the set.
+
+
+
+
+
+
+ Use xnu to mask protein tandem repeats.
+
+
+
+
+
+
+ SEE ALSO
+
+
+ glam2
+ 1
+ ,
+ glam2format
+ 1
+ ,
+ glam2mask
+ 1
+ ,
+ glam2scan
+ 1
+ ,
+ xnu
+ 1
+
+ The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.
+
+
+
+ REFERENCES
+
+ Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618–1632, 1995. Please cite it if you use Purge.
+
+
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+
+
+
--- glam2-1064.orig/debian/examples
+++ glam2-1064/debian/examples
@@ -0,0 +1 @@
+examples/*
--- glam2-1064.orig/debian/changelog
+++ glam2-1064/debian/changelog
@@ -0,0 +1,28 @@
+glam2 (1064-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release
+ - One paragraph added to the tutorial.
+ - Uses CFLAGS in makefiles (thanks Martin!)
+ * Changed the doc-base section according to the new policy.
+ * Updated my email address.
+ * Added a get-orig-source target in debian/rules.
+ * debian/patches/Makefiles removed because obsoleted.
+
+ [ Andreas Tille ]
+ * Better formatting of long description.
+
+ -- Charles Plessy Mon, 19 May 2008 18:46:20 +0900
+
+glam2 (1058-1) unstable; urgency=low
+
+ * New upstream release (Fixes bug in usage message: z_def was out of order.)
+
+ -- Charles Plessy Thu, 14 Feb 2008 13:05:54 +0900
+
+glam2 (1056-1) unstable; urgency=low
+
+ * Initial release (Closes: #45237)
+
+ -- Steffen Moeller Tue, 13 Nov 2007 00:35:50 +0100
+
--- glam2-1064.orig/debian/install
+++ glam2-1064/debian/install
@@ -0,0 +1,5 @@
+src/glam2format /usr/bin/
+src/glam2mask /usr/bin/
+src/glam2scan /usr/bin/
+src/glam2fft /usr/bin/
+purge/purge /usr/bin
--- glam2-1064.orig/debian/glam2.doc-base.manual
+++ glam2-1064/debian/glam2.doc-base.manual
@@ -0,0 +1,13 @@
+Document: glam2-manual
+Title: GLAM2 Manual
+Author: Martin Frith, Timothy L Bailey
+Abstract: This manal covers the installation and
+ usage of GLAM2. It provides a tutorial and a reference
+ for the `glam2' program, a manual for the `glam2scan',
+ `glam2format', `glam2mask' and `purge', as well as
+ explanations about alphabets and Dirichlet mixtures.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/glam2/index.html
+Files: /usr/share/doc/glam2/*.html
--- glam2-1064.orig/debian/glam2format.1
+++ glam2-1064/debian/glam2format.1
@@ -0,0 +1,86 @@
+.\" Title: GLAM2FORMAT
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2
+.\" Date: 05/19/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2FORMAT" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2format \- converts GLAM2 motifs to FASTA or MSF format
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\&.glam2\fR
+.PP
+Formats: fasta, msf\&.
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2format\fR
+reads in a motif found by
+\fBglam2\fR, and writes it in a standard alignment format (FASTA\-with\-gaps or MSF)\&. This enables the alignment to be passed to third\-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo\&. On the other hand, not all the motif information is preserved: in particular, the key positions are lost\&. Only the top motif in
+\fBglam2\fR
+output is converted\&.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\&.
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Make a compact alignment\&. By default, residues that are inserted between key positions are written as unaligned with each other\&. This best reflects
+\fBglam2\fR\'s intention, but it can make the alignment large and full of gaps\&. With
+\fI\-c\fR, inserted residues are written as arbitrarily aligned with each other, just as they appear in the
+\fBglam2\fR
+output\&.
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Sequence file to make a
+\(lqglobal\(rq
+alignment by adding flanking sequences from the original FASTA\-format sequence file\&. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the
+\fI\-c\fR
+option\&. The sequences should have unique names and their order should be unchanged\&.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBboxshade\fR(1),
+\fBglam2\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\&.org\&.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\&.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\&.
+.PP
+\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\&.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\&.
+.sp
--- glam2-1064.orig/debian/copyright
+++ glam2-1064/debian/copyright
@@ -0,0 +1,69 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Steffen Moeller
+Debianized-Date: Tue, 13 Nov 2007 00:35:50 +0100
+Original-Source-Location: http://bioinformatics.org.au/glam2/archive/glam2-1062.zip
+Original-Source-Depends: unzip
+Original-Source-Command: ./debian/rules get-orig-source
+Upstream-Author: Martin C Frith
+ Timothy L Bailey
+
+Files: *
+X-Upstream-Author: 2007 Martin C Frith
+ 2007 Timothy L Bailey
+License: PD
+ GLAM2 was developed by Martin C Frith, working at the Computational Biology
+ Research Center in Tokyo, and Timothy L Bailey, working at the Institute for
+ Molecular Bioscience in Brisbane. The source code and documentation are hereby
+ released into the public domain. If you use GLAM2, please cite: MC Frith, NFW
+ Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary
+ insertions and deletions, PLoS Computational Biology (PLoS Comput Biol. 2008
+ Apr 25;4(4):e1000071.).
+
+Files: purge/*
+X-Upstream-Author: Andrew Neuwald
+License: PD
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software is freely available to the
+ public for use. The National Library of Medicine and the U.S. Government
+ have not placed any restriction on its use or reproduction.
+ .
+ Although reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite
+ .
+ Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling:
+ detection of bacterial outer membrane protein repeats"
+ Protein Science 4, 1618-1632. (for Gibbs site sampling,
+ Gibbs motif sampling, purge, and scan programs)
+ .
+ and
+ .
+ Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993)
+ "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy
+ for Multiple Alignment", Science 262:208-214. (for Gibbs
+ site sampling program)
+ .
+ in any work or product based on this material.
+ .
+ The data structures used in this program are part of a package
+ of C code for molecular biological applications being developed
+ by A. F. Neuwald.
+
+Files: debian/*
+Upstream-Author: 2007 Steffen Moeller
+ 2007-2008 Charles Plessy
+License: PD
+ The package is in the public domain and so shall then be
+ the packaging for Debian of Steffen Moeller
+ and Charles Plessy .
--- glam2-1064.orig/debian/glam2format.1.xml
+++ glam2-1064/debian/glam2format.1.xml
@@ -0,0 +1,140 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+ &dhtitle;
+ &dhproduct;
+ &dhrelease;
+
+
+ Martin
+ C
+ Frith
+ Author of GLAM2.
+
+
+ Timothy
+ L
+ Bailey
+ Author of GLAM2.
+
+
+ &dhfirstname;
+ &dhsurname;
+ Formatted this manpage in DocBook XML for the Debian distribution.
+
+ &dhemail;
+
+
+
+
+ The source code and the documentation of GLAM2 are released in the public domain.
+
+
+
+ &dhucpackage;
+ &dhsection;
+
+
+ &dhpackage;
+ converts GLAM2 motifs to FASTA or MSF format
+
+
+
+ &dhpackage;
+
+
+ my_motif.glam2
+
+ Formats: fasta, msf.
+
+
+
+ DESCRIPTION
+
+ &dhpackage; reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is converted.
+
+
+
+
+ OPTIONS (default settings)
+
+
+
+
+
+
+ Output file (stdout).
+
+
+
+
+
+
+ Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects glam2's intention, but it can make the alignment large and full of gaps. With -c, inserted residues are written as arbitrarily aligned with each other, just as they appear in the glam2 output.
+
+
+
+
+
+
+ Sequence file to make a global alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. The sequences should have unique names and their order should be unchanged.
+
+
+
+
+
+
+ SEE ALSO
+
+ boxshade
+ 1,
+ glam2
+ 1
+ ,
+ glam2mask
+ 1
+ ,
+ glam2-purge
+ 1
+ ,
+ glam2scan
+ 1
+
+ The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/.
+
+
+
+ REFERENCE
+
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+
+
+