amkozlov/raxml-ng: RAxML-NG v0.6.0 BETA

Published June 16, 2018 | Version 0.6.0

Software Open

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

Files

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amkozlov/raxml-ng-0.6.0.zip md5:c0a853a3b21bc7b80d500abdbf056860	123.0 kB	Preview Download