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RAxML-NG v1.0.0
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@amkozlov amkozlov released this 08 Aug 01:23
· 83 commits to master since this release
1.0.0
308ff5c

Major new features

  • coarse-grained parallelization across tree searches (--workers option) -> see details
  • adaptive parallelization (--threads auto{MAX}, --workers auto) -> see detais
  • print per-site log-likelihoods (--sitelh command, #26)
  • alignment column weighting (--site-weights option, #51) -> see details

Other features & optimizations

  • energy monitoring via RAPL -> see details
  • partial loading of RBA alignments (ExaML-style, saves memory for MPI runs on large supermatrices)
  • detect CPU core oversubscription to prevent extreme slowdowns -> see details
  • collapse short branches (bl=min) into multifurcations (#23)
  • write down intermediate results (mlTrees, bootstraps)
  • much faster (20x-30x) parsimony starting tree generation

Bugfixes

  • asc bias failed under certain circumstances (site repeats disabled and non-DNA data)
  • fix zero subst. rates in FLU model (#93)
  • out-of-range branch lengths after scaling/normalization (eg #86)
  • base frequency optimization sporadically failed when estimates hit the boundaries

Minor

  • print CPU model/RAM/core count in logfile
  • if --blmin is specified, adjust --precision accordingly
  • remove BS support + 0.0 brlen at the root
  • ensure that min/max brlens are not exceeded in user starting tree
  • check that --msa file is not empty and not a directory
  • check if start trees are bifurcating (#96)
  • check if partition range has all sites in single-partition case
  • check if +BU{} is specified in single-partition case
  • do not use word "pattern" if pattern compression is off
Assets 6