PhyloBayes
For instructions, see manual
PhyloBayes CM (covarion mixture)
History :
December 16 2015 : version 4.1c. :
added pre-compiled executable files for macOSX
June 8 2015 : version 4.1. :
in readdiv: now possible to get 1-alpha credible intervals for arbitrary values of alpha
prior on the alpha parameter of the gamma distribution now log-uniform (can be reverted to exponential of mean 1 using -expalpha option)
there was a bug in the Dayhoff4 recoding: W and Y mis-recoded as belonging to same category as DENQ instead of hydrophobic
one bug corrected, causing the program to exit when reading nucleotide data on some machines
November 12 2012 : version 3.3f. :
one extra column in trace file under the C20 model removed (causing problems with tracecomp)
July 05 2012 : version 3.3e. :
added an option allowing analysis of datasets based on non canonical state-spaces (alphabets of arbitrary size)
one bug corrected: the mtart and mtzoa models were not activated when requested
one extra column in tracefile removed (causing problems with tracecomp)
some numerical problems under CAT-GTR, when analyzing highly conserved alignments, detected and corrected
March 18 2011 : version 3.3b. :
a new program for ancestral sequence reconstruction
one bug causing memory allocation problems under macOSX corrected
one bug in the saturation test corrected: the homoplasy statistic under non-poisson models was incorrect
several minor optimizations of the code.
September 29 2010 : version 3.2f. :
A bug in the postscript output of readdiv corrected (credibility intervals were incorrect). The credibility intervals in the .chronogram.tre and .dates files were correct. Only the postscript display was wrong.
The default model for the across-site rate variation has changed: it has reverted back to the discrete gamma model.
Several minor optimizations of the code.
April 22 2010 : version 3.2e. :
Corrected : a small bug in readpb (causing a segmentation fault upon leaving the program), and a bug in molecular dating under the GTR or CAT-GTR model.
November 12 2009 : version 3.2d. :
One bug, causing numerical errors upon stopping/restarting a chain, corrected.
September 22 2009 : version 3.2c. :
Introduction of mtZOA and mtART matrices for amino-acid substitutions in metazoa and arthropods (Rota Stabelli et al, 2009).
July 29 2009 : version 3.2b. :
One bug corrected concerning the estimation of the parameter of the dirichlet prior on divergence times in the absence of calibrations.
July 28 2009 : version 3.2. :
Code optimization, leading to a signifcant speed-up of the computations under the birth death prior.
Minor modifications concerning the prior on birth death parameters, so as to allow for easier comparisons with paml.
Extensive rewriting of some sections of the manual, with a separate section now devoted to molecular dating experiments.
IMPORTANT:
a bug concerning the combine use of the -rp option (gamma or exponential prior on the age of the root) and the birth death prior for divergence times was found in versions 3.1c to 3.1h. The bug may have an impact on the estimated ages. It did not concern the birth death without the use of the -rp option.
The birth death prior of version 3.2 has been checked against Paml with and without gamma priors on the root (version 3.1 had been checked against multidivtime and against paml, although not in the specific combination of the birth death and the gamma prior on the root).
July 21 2009 : version 3.1h. : a bug concerning soft bounds corrected.
July 6 2009 : version 3.1g. : a bug was introduced (june 24) in the white noise and uncorrelated gamma models. this is now corrected.
June 24 2009 : version 3.1f. : a few clarifications brought in the options of the pb program.
April 9 2009 : version 3.1d. : Introduction of soft fossil constraints and convergence diagnostics. One bug corrected.
January 26 2009 : version 3.1c.
January 10 2009 : version 3.1.
January 7 2008 : version 2.3c : some extras concerning "-cl" option added in readpb.
December 22 2007 : version 2.3b : a bug concerning the use of
GTR or CAT-GTR for molecular dating corrected.
September 28 2007 : version 2.3 modified for allowing
optional compiling with/without gsl
September 24 2007 : version 2.3
Februrary, 2007 : version 2.1c
January 2007 : version 2.1
May 2006 : version 1.1c