RAxML-NG v0.6.0 BETA

New features

• support for binary (aka presence/absence) and multistate (aka morphological) models
• comprehensive and partial topological constraints (--tree-constraint)
• binary MSA format (a la ExaML)
• phylogenetic terrace detection using terraphast library (thanks to @upsj et al.)
• support for unlinked branch length mode in partitioned analyses (--brlen unlinked)
• automatic MRE-based bootstrap convergence check (also a posteriori with --bsconverge)
• outgroup rooting (--outgoup)

Minor features and optimizations

• separate command to generate starting trees (--start)
• (alias) command to compute tree loglh w/o optimization (--loglh)
• console-only mode (--nofiles)
• user-specified precision for logLH, branch length etc. (--precision)
• --parse command to compress alignment patterns, generate binary MSA and estimate resource requirements (RAM, #threads)
• random/parsimony/user starting trees can be combined in a single program invocation
• parsimony starting trees on mixed-datatype alignments
• faster restart from checkpoint by re-using existing starting trees and binary MSA file
• add missing SSE3 PLF kernels (major speedup on old pre-AVX machines)
• libll and pll-modules are now built with CMake (grand merci @BenoitMorel)

Bugfixes

• fix p-inv optimization in multi-threaded multi-partitioned runs (brent opt param broadcast)
• fix scaled branch length optimization when branches hit min/max value
• better error messages for ill-formatted partition files