diff -Nru fasttree-2.1.9/changelog fasttree-2.1.10/changelog
--- fasttree-2.1.9/changelog	2016-04-20 20:13:57.000000000 +0000
+++ fasttree-2.1.10/changelog	2017-08-18 11:30:32.000000000 +0000
@@ -1,3 +1,14 @@
+Version 2.1.10: April 11, 2017
+
+	Fix a bug when using GTR models with huge alignments with over 2
+	billion non-gap characters. The frequencies of A, C, G, and T were
+	being computed with a 32-bit (signed) counter. This led to
+	negative frequencies and eventually to a crash with
+	"FastTree.c:9769: tqli: Assertion `iter < 30' failed.". SetMLGtr()
+	now uses 64-bit counters. Also, more information about the
+	optimization of the GTR model is savd in the log file (if using
+	the -log option). To support this, gtr_opt_t now includes fpLog.
+
 Version 2.1.9: March 29, 2016
 
 	Add the -lg option to use Le/Gascuel model for amino acid
diff -Nru fasttree-2.1.9/debian/changelog fasttree-2.1.10/debian/changelog
--- fasttree-2.1.9/debian/changelog	2017-06-29 11:46:37.000000000 +0000
+++ fasttree-2.1.10/debian/changelog	2017-09-09 17:00:00.000000000 +0000
@@ -1,3 +1,9 @@
+fasttree (2.1.10-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Thorsten Alteholz <debian@alteholz.de>  Sat, 09 Sep 2017 19:00:00 +0200
+
 fasttree (2.1.9-2) unstable; urgency=medium
 
   * Team upload
diff -Nru fasttree-2.1.9/fasttree.c fasttree-2.1.10/fasttree.c
--- fasttree-2.1.9/fasttree.c	2016-04-20 20:13:54.000000000 +0000
+++ fasttree-2.1.10/fasttree.c	2017-08-18 11:30:30.000000000 +0000
@@ -343,7 +343,7 @@
 
 #endif /* USE_SSE3 */
 
-#define FT_VERSION "2.1.9"
+#define FT_VERSION "2.1.10"
 
 char *usage =
   "  FastTree protein_alignment > tree\n"
@@ -1380,6 +1380,7 @@
   double freq[4];
   double rates[6];
   int iRate;			/* which rate to set x from */
+  FILE *fpLog; /* OPTIONAL WRITE */
 } gtr_opt_t;
 
 /* Returns -log_likelihood for the tree with the given rates
@@ -5848,11 +5849,14 @@
   assert(nCodes==4);
   gtr_opt_t gtr;
   gtr.NJ = NJ;
+  gtr.fpLog = fpLog;
   if (freq_in != NULL) {
     for (i=0; i<4; i++)
       gtr.freq[i]=freq_in[i];
   } else {
-    int n[4] = {1,1,1,1};	/* pseudocounts */
+    /* n[] and sum were int in FastTree 2.1.9 and earlier -- this
+       caused gtr analyses to fail on analyses with >2e9 positions */
+    long n[4] = {1,1,1,1};	/* pseudocounts */
     for (i=0; i<NJ->nSeq; i++) {
       unsigned char *codes = NJ->profiles[i]->codes;
       int iPos;
@@ -5860,7 +5864,7 @@
 	if (codes[iPos] < 4)
 	  n[codes[iPos]]++;
     }
-    int sum = n[0]+n[1]+n[2]+n[3];
+    long sum = n[0]+n[1]+n[2]+n[3];
     for (i=0; i<4; i++)
       gtr.freq[i] = n[i]/(double)sum;
   }
@@ -5903,6 +5907,7 @@
 }
 
 double GTRNegLogLk(double x, void *data) {
+  
   gtr_opt_t *gtr = (gtr_opt_t*)data;
   assert(nCodes == 4);
   assert(gtr->NJ != NULL);
@@ -5915,6 +5920,12 @@
     rates[i] = gtr->rates[i];
   rates[gtr->iRate] = x;
 
+  FILE *fpLog = gtr->fpLog;
+  if (fpLog)
+    fprintf(fpLog, "GTR_Opt\tfreq %.5f %.5f %.5f %.5f rates %.5f %.5f %.5f %.5f %.5f %.5f\n",
+          gtr->freq[0], gtr->freq[1], gtr->freq[2], gtr->freq[3],
+          rates[0], rates[1], rates[2], rates[3], rates[4], rates[5]);
+
   gtr->NJ->transmat = CreateGTR(rates, gtr->freq);
   RecomputeMLProfiles(/*IN/OUT*/gtr->NJ);
   double loglk = TreeLogLk(gtr->NJ, /*site_loglk*/NULL);
@@ -5923,7 +5934,10 @@
   /* Do not recompute profiles -- assume the caller will do that */
   if (verbose > 2)
     fprintf(stderr, "GTR LogLk(%.5f %.5f %.5f %.5f %.5f %.5f) = %f\n",
-	    rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk); 
+	    rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk);
+  if (fpLog)
+    fprintf(fpLog, "GTR_Opt\tGTR LogLk(%.5f %.5f %.5f %.5f %.5f %.5f) = %f\n",
+	    rates[0], rates[1], rates[2], rates[3], rates[4], rates[5], loglk);
   return(-loglk);
 }