Heterotachy model

[bqminh]

The heterotachy model is a mixture model allowing to have separate sets of branch lengths per mixture class, or branch-unlinked mixture models, which generalizes the Gamma as well as FreeRate heterogeneity across sites. It naturally accounts for heterotachous evolution (for more details see http://www.iqtree.org/doc/Heterotachy-Models/). The models will be integrated into version 1.6.0.

Right now the beta-testing implementation is available in the heterotachy branch of the git repository. The run can be invoked by e.g.:

iqtree -s alignment -m GTR+FO+H3

where H for Heterotachy and H3 means 3 heterotachous mixture classes.

Items done (as of Nov 16 2016):

• More user-friendly (e.g. NEWICK tree file without / so that it is readable by common tree viewers).
• Better branch length optimization with multi-dimensional Newton-Raphson instead of the EM algorithm.
• Allow to work transparently with existing mixture models (e.g. the CAT model), so that user can specify something like -m C10+H (CAT profile mixture model, where +H will override the default Gamma model [+G]).
• Allow a proportion of invariable sites with e.g. -m GTR+I+H3.

TODOs:

• Thorough testing, e.g., to make sure that the code does not break down other options.
• Allow model selection to test for +H.

[bqminh]

DONE (2017-12-21)