IQ-TREE version 1.5.0

Oct 24, 2016

We are pleased to announce IQ-TREE version 1.5.0 with following major updates:

Major new features:

A new posterior mean site frequency (PMSF) model as a rapid approximation to the time and memory consuming CAT profile mixture models C10 to C60 (Le et al., 2008a). The PMSF model is much faster and requires much less RAM than the mixture models, regardless of the number of mixture classes. This allows, for the first time, to conduct nonparametric bootstrap under such complex models. Our extensive simulations and empirical deep-phylogeny data analyses demonstrate that the PMSF models can effectively ameliorate long branch attraction artefacts. For details see http://www.iqtree.org/doc/Complex-Models/#site-specific-frequency-models
New option -g to supply a user-defined constraint tree, which will guide subsequent tree search. The constraint tree can be multifurcating and need not to include all taxa.

Bug fixes:

Crash with zero weights of mixture models for short alignments (thanks to Laura Eme for the report).
Incorrect site rate file (-wsr option) in the presence of identical sequences (thanks to Brian Foley for the report).
Memory overflow for tree topology testing for extremely long alignments (>500,000 sites) (thanks to Karen Meusemann for the report).
Rare issue with multifurcating trees and partition model (thanks to Xingxing for the report).

Other changes:

A new biologist-familiar example data file example.phy, which contains mitochondrial DNAs of human, gorilla, dog, mouse, etc. The data set was taken from the phylogenetic handbook (thanks to Brian Foley for suggestion).
Printing an alignment with suffix .varsite with only variable sites if ascertainment bias correction (ASC) is not applicable.
New option -wpl to write partition-specific log-likelihoods to .partlh file (requested by Karen Meusemann).