amkozlov/raxml-ng: RAxML-NG v0.7.0 BETA

Published October 22, 2018 | Version 0.7.0

Software Open

New features

new support measure: Transfer Bootstrap Expectation (Lemoine et al., Nature 2018) : use --bs-metric tbe
print AIC/AICc/BIC scores

Minor features and optimizations

IMPORTANT: site repeats are now enabled by default (in case of problems: add --tip-inner on & please report!)
improved load balancing: weight sites according to # states and # rate categories (in case of problems: add --extra lb-kassian & please report!)
thread pinning by default in hybid MPI/pthread mode (--extra thread-nopin to disable)
remove gap-only & duplicate sequences from the reduced alignment file
build parsimony trees in master rank only
check for invalid symbols (spaces,semicolons etc.) in taxon names (problems with Newick)

Bugfixes

IMPORTANT: --support command was broken in v0.6.0, printing BS support values of 0
improve base frequency normalization in empirical AA models (#46, thanks to @bredelings )
increase precision of WAG rates (thanks to @bredelings )
check for terraces only in --brlen unlinked mode
fix model optimization with fixed branch lengths (--evaluate --opt-brances off)
fully resolved/bifurcating constraint tree was ignored (reported by Lois Rancilhac)
fix overflow in site repeats on very large unpartitioned alignments

Files

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amkozlov/raxml-ng-0.7.0.zip md5:aae11d3d76634789515990fd38c8a555	135.4 kB	Preview Download