Ancestral sequence reconstruction

[bqminh]

Computing the ancestral sequences as well as ancestral state probabilities of all internal nodes for a given tree. Although this was long implemented in several programs, including very good Tal Pupko's FastML, they do not provide the variety of models available in IQ-TREE. A marginal state probabilities computation is straight-forward and was already implemented.

iqtree -s alignment -te user_tree -asr

TODOs (as of Sept 8, 2016):

• Joint reconstruction for rate homogeneity model http://mbe.oxfordjournals.org/content/17/6/890.full and for rate heterogeneity model http://bioinformatics.oxfordjournals.org/content/18/8/1116.abstract.

[bqminh]

Done in latest v1.6. Joint reconstruction will not be implemented due to its code complexity.