IQ-TREE version 1.5.4

Apr 3, 2017

Important changes:

If no model is specified via -m, IQ-TREE will perform the new model selection, ModelFinder (MF). Accordingly, two new options are introduced: -m MF (equivalent to -m TESTNEWONLY) and -m MFP (equiv. to -m TESTNEW). For backward compatibility TESTNEW will still be available but might be removed in a future release.
Combining standard bootstrap (-b) and constraint tree option (-g) will impose the constraint on bootstrap trees (previously not). Thanks to Matthew Prebus for discussions.

New features:

The precompiled Linux executables are now backward compatible with the old Linux kernel 2.X, which resolves the error message “FATAL: kernel too old”.
Support input files with different newline formats to resolve conflicts between Mac, Windows or Linux files.
For data sets with identical sequences, redundant sequences are ignored. However, IQ-TREE will now keep two identical sequences (i.e. if five sequences A,B,C,D,E are identical to each other, then A,B are kept and C,D,E are ignored). This avoids incompatibility between bootstrap and non-bootstrap runs.
Warning about too many threads for short alignments (reported by Joran Martijn).
New option -wbsf to print individual bootstrap alignments and sitefreq files for standard bootstrap (requested by Huaichun Wang).

Bug fixes:

Segfault caused by combining standard bootstrap, partition model and constraint tree (reported by Matthew Prebus).
Crash by -nni1 option (reported by Carlos Rivera).
Illegal instruction on older Mac which does not support AVX instruction set (reported by Richard Moir and Matthew Fullmer).
Crash when combining -mtree and -bb during model selection (reported by Chris Buddenhagen).