IQ-TREE version 0.9.6

Oct 20, 2013

Beta version 0.9.6 and earlier versions:

  • Ultrafast (partition) model selection for phylogenomic alignments.
  • Higher accuracy in tree reconstruction and bootstrap with more thorough nearest neighbor interchange enabled via -nni5 option (optimizing 5 branches around NNI). This comes at the trade-off of c.a. 2X longer running time.
  • Introduction of joint and proportional partition models to reduce the number of parameters in case of model overfitting (EXPERIMENTAL)
  • Introduction of gene-resampling and gene-and-site resampling for the bootstrap on multi-gene alignments.
  • Introduction of epsilon for ultrafast bootstrap: trees similar RELL log-likelihoods will be chosen at random to break tie. This helps to reduce over-optimistic supports in case of polytomies.
  • Tree topology tests (BP,KH,SH,ELW,WKH, and WSH tests via RELL method).
  • Partition models.
  • Parallel OpenMP version for multi-core CPUs.
  • New implementation of model selection that works for DNA, amino-acid, and binary models.
Download version 0.9.6 from GitHub

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