IQ-TREE version 1.5.5

Jun 2, 2017

New features:

  • Support gene-resampling (-bsam GENE) and gene-site-resampling (-bsam GENESITE) for standard bootstrap with partition models.
  • Support and treat polymorphic characters in (...) or {...} notation as missing data (requested by Steven Heritage).
  • Improved numerical stability for codon models (reported by Giorgio Matassi, Sarah Mathews, Ricardo Alves). Note that numerics may still fail if many codons are absent in the data.
  • Do not test ascertainment bias correction (+ASC) for codon models by default (thanks Ricardo Alves).
  • Only reduce minimal branch length for long alignment and un-partition models (thanks to Steven Mussmann).


  • Initial tree generation problem with constrained tree search option -g.
  • Likelihood underflow for large multifurcating trees (e.g. consensus tree) (reported by Giap Nguyen).
  • Crash with -minsupnew option (reported by Longzhi Tan).
  • Compilation with gcc under Mac (thanks @ilovezfs).
  • Crash with -nni1 for partition model -spp (reported by Diep Thi Hoang).
Download version 1.5.5 from GitHub

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