IQ-TREE version 1.4.4

Aug 28, 2016

New features:

• Allowing mixture frequency model with optimized frequency via e.g. -m C10+FO (requested by Edward Braun).
• Supporting GTR20 (general time reversible) amino-acid model (requested by Desmond Ramirez, Panagiotis Adam).
• New option -blscale to optimize tree length scaling factor and model parameters for a user tree passed via -t option (requested by Rob Lanfear). The results are written to .blscale file in YAML format.
• New option --no-outfiles to suppress printing all output files (.log, .treefile, .iqtree files).

Bug fixes:

• (critical) Memory overflow for long alignments (>55,000 aa site patterns) under large mixture models (e.g. C60) (reported by Matthew Brown).
• (critical) AU test implementation (reported by Jan Janouskovec).
• Counting of constant sites with many ambiguous states (reported by Greg Owens).

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