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.

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