RAxML-NG v1.0.0

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