IQ-TREE version 1.3.3

Jun 27, 2015

We are pleased to announce version 1.3.3 with substantial improvements:

• Implement the relaxed clustering algorithm of PartitionFinder with -rcluster option to speed up analysis for data sets with many partitions (e.g., >100 partitions).
• Partition finding supports multicore now with linear speedup.
• Increased multicore performance of partition model analysis.
• Support direct translation of coding sequences into amino-acid (-st NT2AA option).
• Adjust per-partition state frequencies for partition model such that the log-likelihoods are fully comparable with RAxML.
• Print sequence identity scores along the tree (-wsi option).
• Fix slow convergence of partition model parameter estimation with many partitions.
• Fix memory allocation for large mixture models.

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