IQ-TREE version 1.3.11

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.