MCaa.dat

@@ -8,7 +8,7 @@
 (((Human:0.06135, Chimpanzee:0.07636):0.03287, Gorilla:0.08197):0.11219, Orangutan:0.28339, Gibbon:0.42389);
 
 .5 8        * <alpha; see notes below>  <#categories for discrete gamma>
-2 mtmam.dat * <model> [aa substitution rate file, need only if model=2 or 3]
+2 dat/mtmam.dat * <model> [aa substitution rate file, need only if model=2 or 3]
 
 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 
 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 

MCbase.dat

- 0     * 0,1:seqs or patterns in paml format (mc.paml); 2:paup format (mc.nex); 3: paup JC69 format
- -1234567   * random number seed (odd number)
+ 1     * 0,1:seqs or patterns in paml format (mc.paml); 2:paup format (mc.nex); 3: paup JC69 format
+ -123  * random number seed (odd number)
 
 5 895 100  * <# seqs>  <# nucleotide sites>  <# replicates>
 -1         * <tree length, use -1 if tree below has absolute branch lengths>

aaml.ctl

-      seqfile = D:\A\MySoft\paml4.6\stewart.aa
-     treefile = D:\A\MySoft\paml4.6\stewart.trees
+      seqfile = stewart.aa
+     treefile = stewart.trees
 
       outfile = mlc
         noisy = 9

baseml.ctl

@@ -7,14 +7,14 @@
       runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic
                     * 3: StepwiseAddition; (4,5):PerturbationNNI 
 
-        model = 7   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
+        model = 4   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
                     * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
 
         Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
 
 *        ndata = 100
         clock = 0   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
-    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below
+    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below; 2: kappa for branches
         kappa = 5  * initial or fixed kappa
 
     fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
@@ -30,5 +30,5 @@
    Small_Diff = 7e-6
     cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
 *        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)
-*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
        method = 0  * Optimization method 0: simultaneous; 1: one branch a time

codeml.ctl

@@ -48,7 +48,7 @@
 
    Small_Diff = .5e-6
     cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
-*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
+*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
        method = 0  * Optimization method 0: simultaneous; 1: one branch a time
 
 * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,

debian/changelog

+paml (4.9g+dfsg-1) unstable; urgency=medium
+
+  * New upstream version (upstream fixed format security issue)
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * do not parse d/changelog
+
+ -- Andreas Tille <tille@debian.org>  Fri, 16 Feb 2018 11:57:07 +0100
+
 paml (4.9e+dfsg-1) unstable; urgency=medium
 
   * This new upstream version is now covered by a free license and can

debian/compat

-9
+11

debian/control

@@ -5,8 +5,8 @@ Uploaders: Pjotr Prins <pjotr.debian@thebird.nl>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.8
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/paml.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/paml.git
 Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html

debian/patches/fix_format_security.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 30 Jul 2014 14:30:38 +0200
-Description: Fix some format security issues
-
---- a/src/mcmctree.c
-+++ b/src/mcmctree.c
-@@ -327,7 +327,7 @@ int GetMem (void)
-          error2("oom conP");
- 
-       com.conPin[1] = com.conPin[0] + com.sconP/sizeof(double);
--      printf("\n%u bytes for conP\n", 2*com.sconP);
-+      printf("\n%u bytes for conP\n", 2*(unsigned)com.sconP);
- 
-       /* set gnodes[locus][].conP for tips and internal nodes */
-       com.curconP = 0;

debian/patches/series

-fix_format_security.patch
 hardening.patch
 add_clean_target.patch

debian/rules

@@ -5,7 +5,8 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
-DEBPKGNAME:=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+include /usr/share/dpkg/default.mk
+
 DATADIR=/usr/lib/paml/data
 
 %:
@@ -20,20 +21,20 @@ override_dh_installexamples:
 override_dh_install:
 	dh_install
 	set -x ; \
-	for datfile in debian/$(DEBPKGNAME)/$(DATADIR)/*.ctl ; do \
+	for datfile in debian/$(DEB_SOURCE)/$(DATADIR)/*.ctl ; do \
 	    for item in seqfile treefile ; do \
 		sed -i -e "s?\($${item} =\).*[^a-z^A-Z^0-9^.^ ]\+\([a-zA-Z0-9]\+\.[a-z]\+\)?\1 $(DATADIR)/\2?" \
 		       -e "s?\($${item} =\) \([a-zA-Z0-9]\+\.[a-z]\+\)?\1 $(DATADIR)/\2?" \
 		       $${datfile} ; \
 	    done ; \
 	done
-	sed -i 's?\(aaRatefile = \)\(dat/jones.dat\)?\1$(DATADIR)/\2?' debian/$(DEBPKGNAME)/$(DATADIR)/codeml.ctl
+	sed -i 's?\(aaRatefile = \)\(dat/jones.dat\)?\1$(DATADIR)/\2?' debian/$(DEB_SOURCE)/$(DATADIR)/codeml.ctl
 
 override_dh_link:
 	dh_link
-	mkdir -p debian/$(DEBPKGNAME)/etc/$(DEBPKGNAME)/
-	for datfile in debian/$(DEBPKGNAME)/$(DATADIR)/*.ctl ; do \
-	    ln -s $(DATADIR)/`basename $${datfile}` debian/$(DEBPKGNAME)/etc/$(DEBPKGNAME) ; \
+	mkdir -p debian/$(DEB_SOURCE)/etc/$(DEB_SOURCE)/
+	for datfile in debian/$(DEB_SOURCE)/$(DATADIR)/*.ctl ; do \
+	    ln -s $(DATADIR)/`basename $${datfile}` debian/$(DEB_SOURCE)/etc/$(DEB_SOURCE) ; \
 	done
 
 override_dh_fixperms:

doc/pamlHistory.txt

@@ -9,20 +9,87 @@ https://groups.google.com/forum/#!forum/pamlsoftware.
 
 
 
+Version 4.9g, December 2017
+
+(*) codeml.  A bug caused the BEB calculation under the site model M8
+(NSsites = 8) to be incorrect, with the program printing out warming
+messages like "strange: f[ 5] = -0.0587063 very small."  This bug was
+introduced in version 4.9b and affects versions 4.9b-f.  A different
+bug was introduced in version 4.9f that causes the log likelihood
+function under the site model M8 (NSsites = 8) to calculated
+incorrectly.  These are now fixed.
+
+
+
+Version 4.9f, October 2017
+
+(*) baseml, nonhomogeneous models (nhomo & fix_kappa).  Those models
+allow different branches on the tree to have different Q matrices.
+Roughly nhomo controls the base frequency parameters while gix_kappa
+controls kappa or the exchangeability parameters (a b c d e in
+GTR/REV, for example).  I added the option (nhomo = 5, fix_kappa = 2),
+which lets the user to define branch types, so that branches of the
+same type have the same exchangeability parameters (a b c d e for GTR)
+and base composition parameters, while branches of different types
+have different parameters.  Branch types are labeled (using # and $),
+0, 1, 2, ....  The labels should be consecutive positive integers.
+The old options nhomo = 3 or 4 work for some models like GTR, but not
+some other models which also have base composition parameters.  In
+this update, I think those options should work with all those models.
+I have also edited the documentation (look for option variable nhomo
+for baseml).
+
+
+(*) baseml & codeml.  i added an option fix_blength = 3
+(proportional), which means that branch lengths will be proporational
+to those given in the tree file, and the proportionality factor is
+estimated by ML.
+
+(*) codeml.  The program does not count the parameters correctly for
+model M0 when fix_kappa = 1.  The bug was introduced in version 4.9c
+and affects versions 4.9c-e.  This is now fixed.
+
+(*) codeml (seqtype = 2 model = 2).  If you are analyzing multiple
+protein data sets (ndata > 1) under the empirical models such as wag,
+jtt, dayhoff.  The results for the first data set are correct, but all
+later data sets are analyzed incorrectly under the corresponding +F
+models, that is, wag+F, jtt+F, dayhoff+F, etc.  A bug in the program
+means that for the second and later data sets, the equilibrium amino
+acid frequencies are taken from the real data and not correctly set to
+those specified by the empirical models.  I note that this bug was
+recorded in the update Version 3.14b, April 2005, but it was somehow
+not fixed, even in that version.  This is now fixed.  Thanks to Nick
+Goldman for reporting this again.
+
+(*) evolver (options 5, 6, 7 for simulating nucleotide, codon and
+amino acid alignments).  If you choose the option of printing out the
+site pattern counts instead of the sequences (specified at the
+beginning of the control file such as MCbase.dat), and if you are
+simulating two or more alignments, the program crashes after finishing
+the first alignment.  This is now fixed.
+
+(*) mcmctree.  The program crashes if you have a mixture of
+morphological loci and molecular loci, if not all the morphological
+loci are before the molecular loci.  I have now fixed this.  
+I think this was never described anyway.
+
+
+
 Version 4.9e, March 2017
 
-Edited the readme files to change the license to GPL.
+(*) Edited the readme files to change the license to GPL.
 
+(*) mcmctree.  A bug was introduced in version 4.9b which causes the
+program to read the fossil calibration information in the tree file
+incorrectly, if joint (minimum and maximum) bounds are specified using
+the symbol '<' and '>'.  If you use the notation "B()", "L()", and
+'U()', the information is read correctly.  This bug was introduced in
+version 4.9b and exists in 4.9c and 4.9d.  Versions 4.9a and earlier
+were correct.
 
 
-Version 4.9d, February 2017
 
-(*) mcmctree.  A bug was introduced which causes the program to read
-the fossil calibration information in the tree file incorrectly, if
-lower (minimum) bounds are specified using the symbol '>'.  If you use
-the notation "B()" or "L()", the information is read correctly.  This
-bug was introduced in version 4.9b and exists also in 4.9c.  Versions
-4.9a and earlier were correct.
+Version 4.9d, February 2017
 
 (*) mcmctree.  Changed the default prior for rates for loci to
 gamma-Dirichlet (dos Reis 2014), and updated the documentation as
@@ -37,7 +104,6 @@ the prior (when beta is small).
 
 
 
-
 Version 4.9c, September 2016
 
 (*) Added GPL license statement in various places.

examples/DatingSoftBound/mtCDNApri.trees

  7  1
 
+
 ((((human, (chimpanzee, bonobo)) '>.06<.08', gorilla),
 (orangutan, sumatran)) '>.12<.16', gibbon);
 

examples/HIVNSsites/codeml.ctl

@@ -30,4 +30,4 @@
 
    Small_Diff = .45e-6
     cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
-  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed
+  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

examples/lysin/codeml.ctl

@@ -32,3 +32,4 @@
    Small_Diff = 3e-7
     cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
        method = 0  * 0: simultaneous; 1: one branch at a time
+*  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

examples/lysozyme/lysozymeLarge.ctl

@@ -37,3 +37,4 @@
    Small_Diff = .5e-6
 *    cleandata = 1
 *       method = 1   * 0: simultaneous; 1: one branch at a time
+  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

examples/lysozyme/lysozymeSmall.ctl

@@ -30,6 +30,7 @@
         getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
  RateAncestor = 0   * (1/0): rates (alpha>0) or ancestral states (alpha=0)
        method = 0   * 0: simultaneous; 1: one branch at a time
+  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional
 
 
 * Specifications for duplicating results for the small data set in table 1

examples/lysozyme/lysozymeSmall.trees

-    1
-
-
-((Hsa_Human, Hla_gibbon),((Cgu/Can_colobus, Pne_langur) '#1', Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); / * table 1B&F */
+    2
 
+((1,2) #1, ((3,4), 5), (6,7) );        / * table 1C&G */
+((1,2) #1, ((3,4) #1, 5), (6,7) );     / * table 1D&H */
 
-// end of file
 
 
 
-((Hsa_Human: 0.02556, Hla_gibbon: 0.03889): 0.06798,
-((Cgu/Can_colobus: 0.04379, Pne_langur: 0.05254) #1 : 0.07637, Mmu_rhesus:
-0.02168): 0.04345, (Ssc_squirrelM: 0.04080, Cja_marmoset: 0.02392):
-0.12266);
+// end of file
 
 ((Hsa_Human, Hla_gibbon),((Cgu/Can_colobus, Pne_langur) #1,
 Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); / * table 1B&F */

examples/mtCDNA/codeml.ctl

@@ -32,3 +32,4 @@
    Small_Diff = .5e-6
      cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?
         method = 0   * 0: simultaneous; 1: one branch at a time
+   fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional