Testing version 1.4.0-beta3

NOTE: This is a beta version for testing purpose. Please send feedback if you think it does not produce the results as expected, e.g., when compared with IQ-TREE 1.3.X, TREE-PUZZLE or CONSEL.

Updates in beta3:

• Fix a numerical issue when computing maximum likelihood distances (reported by Giap Nguyen)

Updates in beta2:

• Fix a bug in likelihood mapping (reported by Giap Nguyen)
• Support partition models for likelihood mapping

New features:

• Checkpointing: If an IQ-TREE run was stopped for whatever reason, rerunning it with the very same command-line will automatically recover and continue the previous run. If a run successfully finished, IQ-TREE will deny to rerun and issue an error message. In such cases, one can start a new run using another prefix (-pre option) or tell IQ-TREE to overwrite all output files (-redo option).

• Implementation of the likelihood mapping approach (Strimmer and von Haeseler, 1997) to assess the phylogenetic information of an input alignment via -lmap option, which specifies the number of quartets to be drawn randomly. Compared with the original implementation of TREE-PUZZLE, this implementation supports many more substitution models available in IQ-TREE (incl. partition and mixture models). Example usage:

  iqtree -s example.phy -m GTR+G -n 0 -lmap 10000
  

  The likelihood mapping plot will be printed to .svg and .eps file. The report file .iqtree will contain a new section LIKELIHOOD MAPPING STATISTICS for the results.

• Implementation of the approximately unbiased (AU) test (Shimodaira, 2002) via -au option. Compared with the original implementation of CONSEL, this implementation is partition-aware (i.e., bootstrap resampling sites within partitions). Example usage:

  iqtree -s example.phy -m GTR+G -n 0 -z example.trees -zb 10000 -au