IQ-TREE version 1.3.0

May 20, 2015

We are pleased to announce version 1.3.0 with following major updates:

Support for ClustalW and MSF alignment file formats and RAxML-styled partition file format.
With Lars Jermiin group we developed a new model selection strategy, which is invoked via option -m TESTNEW or -m TESTNEWONLY. Among others, it uses the FreeRate model (Yang, 1995; Soubrier et al., 2012) as replacement for the problematic I+G model. FreeRate model is also implemented in PhyML and BEAST 2.
Improved codon model implementation, which is more compatible with codonPhyML, e.g. including models of (Kosiol et al., 2007).
Codon model selection now allows up to 60 codon models to be tested!
Improved support for mixture models.
Accepting two new amino-acids: U (Selenocysteine; treated as unknown character) and J (I or L).
Several bug fixes, including a bug in FreeRate model optimization found and fixed by Thomas Wong and Lars Jermiin.