Apr 3, 2017
-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
TESTNEWwill still be available but might be removed in a future release.
-b) and constraint tree option (
-g) will impose the constraint on bootstrap trees (previously not). Thanks to Matthew Prebus for discussions.
-wbsfto print individual bootstrap alignments and sitefreq files for standard bootstrap (requested by Huaichun Wang).
-nni1option (reported by Carlos Rivera).