Dec 10, 2015
-blmaxoption for min and max branch length (requested by Hang Phan).
-wslmroptions to print site log-likelihood per mixture class and per mixture+rate category, respectively (requested by Huaichun Wang).
--link-alphaoption to link Gamma shape parameter (alpha) across partitions (requested by Huaichun Wang).
+ASCmodel for protein data: disabled now by default (reported by several web server users and Lars Jermiin).
-spwhen changing to old kernel.
-t RANDOMinitial model parameters will now be estimated on a parsimony tree (thanks to Jesse Breinholt for the report and suggestion).
~as an unknown character in the alignment.