IQ-TREE version 1.3.11

Dec 10, 2015

New features:

For long alignments (>100,000 sites) the minimal branch length is now reduced to 0.1/alignment_length to accommodate analysis of very closely related sequences (thanks to David Wyllie for testing).
New -blmin and -blmax option for min and max branch length (requested by Hang Phan).
New -wslm and -wslmr options to print site log-likelihood per mixture class and per mixture+rate category, respectively (requested by Huaichun Wang).
New --link-alpha option to link Gamma shape parameter (alpha) across partitions (requested by Huaichun Wang).

Bug fixes:

Numerical problems with +ASC model for protein data: disabled now by default (reported by several web server users and Lars Jermiin).
Fix a rare crash for option combination -z and -sp when changing to old kernel.
Fix a crash with multicore version with own parsimony kernel (reported by Joan).
Fix a minor issue when outputting mixture model name in model testing (reported by Sophie Abby).
Fix a numerical problem with model testing (reported by Jana).
For -t RANDOM initial model parameters will now be estimated on a parsimony tree (thanks to Jesse Breinholt for the report and suggestion).

Other changes:

Windows AVX version (reported by Aaron Dickey) crashed due to a stack unalignment issue of TDM-GCC compiler (thanks to Agner Fog for suggestion). As a solution, all Windows binaries are now built with Clang.
Updated the latest vectorclass library of Agner Fog.
Print error instead of abort when applying branch tests for multifurcating trees.
Implement EM algorithm for mixture+FreeRate model.
Accept ~ as an unknown character in the alignment.
Code optimization resulting in 5%-10% reduction in running time.