IQ-TREE release 1.3.11

[Bui Quang Minh]

Dear all,

IQ-TREE version 1.3.11 is just released with following changes (http://www.cibiv.at/software/iqtree/release/):

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.

Best,

IQ-TREE development team