RAxML-NG v0.8.0 BETA

IMPORTANT: New defaults

• 20 starting trees = 10 random + 10 parsimony (was: 1 random)
• scaled/proportional branch length model for partitioned alignments (was: linked)
• autoMRE bootstopping (was: 100 BS replicates)

New features

• Robinson-Foulds distance computation (--rfdist / --rf)
• print bootstrap replicate MSAs (--bsmsa)
• flexible MSA character maps for multistate data (see here)
• new AA substitution model: DEN (Kim 2018)

Bugfixes

• when using multiple starting trees, raxml.bestModel file used to store model params from the last tree search and not the one that yielded the best-scoring tree
• deadlock in --loglh with multiple threads
• fix CLV scaling with p-inv models (RAxML/ExaML seem to have this issue as well)
• duplicate taxon name check was broken since v0.7.0 (reported by Terry Jones)

Minor

• account for hyper-threading when detecting the number of CPU cores
• improve error messages for FASTA/PHYLIP formatting issues
• check if --prefix directory exists
• disable overfitting check for single-gene alignments