IQ-TREE version 1.6.0

Dec 23, 2017

This is the major update of the IQ-TREE software for phylogenomic reconstruction.

IMPORTANT: The checkpoint file is no more compatible with 1.5.X, 1.6.betaX or earlier versions. An error message will be printed if you try to recover the run from old versions. Sequential and multicore versions are merged, thus iqtree-omp executable becomes iqtree.

Notable new features:

• Polymorphism-aware models accounting for incomplete lineage sorting (code contributed by Dominik Schrempf).
• Lie Markov and non-reversible models (code contributed by Michael Woodhams).
• Heterotachy models accounting for rate variation across sites and lineages.
• ModelFinder is redesigned to be more flexible. ModelFinder now supports edge-linked partition model selection. It also allows Lie Markov models, heterotachy (+H) models, PoMo models. ModelFinder now uses checkpoint file .model.gz to save space.
• Xeon Phi Knights Landing (AVX-512) support with 2X or more speedup.
• New option -fast to match the speed of FastTree program while still obtaining better trees.
• New option -bnni to further optimize UFBoot trees by nearest neighbor interchange (NNI) directly on corresponding bootstrap alignments (UFBoot2+NNI).
• New option -asr for ancestral sequence reconstruction written to .state file.
• New option -rclusterf to perform fast relaxed clustering algorithm of PartitionFinder2.
• New option -rcluster-max to limit maximum number of partition pairs for merging with rcluster algorithm.

New features:

• New option -alninfo to print alignment sites statistics to .alninfo file (requested by Federico Gaiti).
• For PMSF first fitting step: increase epsilon from 0.01 to 0.1, leading to 2x-3x speedup.
• New option -czb to collapse zero branches, useful by bootstrapping with polytomy.
• For standard bootstrap, branch lengths of consensus tree are now optimized on original alignment (requested by Tim).
• Report mixture model component in .iqtree file if necessary (requested by Joran Martijn).
• Three new mitochondrial protein matrices mtMet, mtVer, mtInv (https://doi.org/10.1186/s12862-017-0987-y). Code contributed by @cuongbb.
• Support alignments in gzipped format.
• -wql option now prints quartet area and corner in .quartetlh file (requested by Karen Meusemann).
• Support GENE resampling (-bspec GENE) and GENESITE resampling (-bspec GENESITE) for standard bootstrap with partition models.

New features for PoMo models:

• Allow PoMo plus Gamma rate model (+P+G).
• Allow bootstrapping with PoMo.
• Improved numerical stability.

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