Amino-acid frequencies of DAYHOFF, DCMUT, JTT, MTREV, WAG, CPREV, LG, MTZOA, PMB, JTTDCMUT, FLU are modified with higher precision and normalised to 1 (thanks Ben Redelings). This may lead to tiny change in log-likelihood (i.e. from 3 digit after comma) but does not affect +F model.
Support ‘.’ syntax for alignment length in partition file (requested by Teofil Nakov).
Crash with -bnni option and GENE/GENESITE resampling (reported by Emmanuel Cantu).
Incorrect WARNING about bootstrap convergence with -bnni option (reported by Max_IT).
Numerical issue with likelihood scaling for gcc under -O3 optimisation.
Handling fixed substitution rates (reported by @bbuchfink).