PhyloBayes MPImanual For additional details about the model and the algorithms, see supplementary information
May 9 2016 : version 1.7a.
A bug in posterior predictive simulations corrected. Some options added and default behavior of program changed for drawing site-specific random variables during posterior predictive simulations. Details about posterior predictive simulations added in manual. A few additional options added for reading chains.
December 9 2015 : version 1.6j.
corrected a bug that was causing problems when reading data files on some machines (error: does not recognize characteminor changes; a few updates on the use of mutation-selection codon models. some other minor changes.
October 31 2013 : version 1.5a.
minor changes; a few updates on the use of mutation-selection codon models.
June 17 2013 : version 1.4f.
very minor changes; one bug with the chronometer corrected.
April 9 2013 : version 1.4e.
improved numerical methods, leading to a change in the prior on the concentration parameter of the Dirichlet process (in version 1.3, the prior was truncated below, in order to avoid numerical instabilities; this constraint has been removed, see supplementary information for more details). Other minor changes and adaptations.
January 31 2013 : version 1.3b.
readpb_mpi, tracecomp and bpcomp now have a default burnin of 20% of the total length of the chain(s); the -s option for saving the entire parameter configuration is not necessary anymore: by default, everything is saved; several problems with posterior predictive checking have been fixed; other various and minor changes and adaptations.
November 26 2012 : version 1.2f.
-rr option did not work properly (now fixed).
November 13 2012 : version 1.2e.
A few details of the user interface (concerning model selection) have been fixed: to prevent misunderstanding about the chosen model, exchangeabilities and mixture type should now always be jointly specified. For instance, the LG model is : -lg -ncat 1 (and not just -lg), and the CAT model is -cat -poisson (and not just -cat).
November 12 2012 : version 1.2d.
November 05 2012 : version 1.2c.