IQ-TREE version 1.6.4

Apr 30, 2018


  • New option --runs to perform multiple tree searches (issue #64 requested by David Maddison). This is motivated by a recent evaluation (Zhou et al. 2018) showing that 10 independent runs outperformed single run in terms of likelihood maximisation.
  • Print branch lengths scaled in number of substitutions for PoMo models.
  • Support specifying 6 GTR rates and G-T rate to be zero from command line (requested by Ben Redelings).
  • New option --show-lh to compute tree log-likelihood without parameter optimisation (issue #67).


  • Fix compilation with gcc 4.8.
  • Incorrect parsing +P for PoMo model string (thanks Carolin Kosiol).
  • Issue #66: Incorrect frequency mixture model when coupled with GTR20 (reported by Dominik Schrempf).
  • .ufboot trees file contains partial branch supports by combination of -bb and -alrt (reported by Guifre Torruella Cortes).
  • Crash in likelihood computation for +ASC model when some states are rare (reported by Paul Madeira).
  • Numerical instability for codon models by reducing upper bound of omega/kappa from 100 to 50 (reported by Aleksas Lab).
  • Crash reading DNA model from file (reported by Benjamin Redelings).
  • Crash with -z option with rooted trees in the presence of identical sequences (reported by cjp1043).
Download version 1.6.4 from GitHub

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