PhyloBayes MPI

Download PhyloBayes MPI 1.7

History :

-  August 1 2016 : version 1.7b. 

Files now hosted on github. History of modifications of the code now available through 'git log'.

-  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.