IQ-TREE version 1.3.9

Sep 29, 2015

We are pleased to announce version 1.3.9 with following notable changes:

• Several bug fixes improving software stability. Special thanks to Xiaofan, Karen Meusemann, Jozsef Bakonyi, Renee, Peter Hosner for reporting bugs.
• A more stable expectation-maximization (EM) algorithm is implemented to optimize parameters of the FreeRate [+R] and LG4X model. Special thanks to Edward Susko, Thomas Wong and Lars Jermiin.
• Several new features (requested by users):
  • Option -wbtl to write bootstrap tree file (.ufboot) with branch lengths.
  • Option -madd to include mixture models into model selection procedure (e.g. -madd LG4M,LG4X).
  • Option -alrt 0 to perform the parametric approximate likelihood ratio (aLRT) branch test (Anisimova and Gascuel, 2006).
  • Option -abayes to perform the parametric aBayes branch test (Anisimova et al., 2011).
• Maximum number of partitions is increased to 16384 instead of 1024.

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