IQ-TREE version 1.6.4

News:

• 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).

Bugfixes:

• 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).