Provided by: bali-phy_3.3+dfsg-1_amd64
trees-consensus – Find consensus trees and supported splits.
trees-consensus [OPTIONS] sampled-trees [sampled-trees ... sampled-trees]
Find consensus trees and supported splits.
-h, –help Produce help message. -s arg (=10%), –skip arg (=10%) Number of trees to skip. -u arg, –until arg Read until this number of trees. -m arg, –max arg Thin tree samples down to this number of trees. -x arg (=1), –subsample arg (=1) Factor by which to subsample. –ignore arg Comma-separated list of taxa to ignore.
–map-trees arg (=1) Only report the top trees per file. –map-tree arg Write out the map tree to file . –min-support arg (=0.25) Minimum threshold PP for splits. –report arg Write supported partitions to file . –consensus-PP arg Write out consensus trees+PP. –consensus arg Write out consensus trees. –greedy-consensus arg Write out greedy consensus trees. –extended-consensus-L arg Write out extended consensus trees + lengths. –extended-consensus arg Write out extended consensus trees. –support-levels arg Write #branches versus LOD to file . –extended-support-levels arg Write #sub-branches versus LOD to file . –odds-ratio arg (=1.5) Report partial-splits only if removing taxa improves the odds by at least this ratio. -v, –verbose Output more log messages on stderr.
–sub-partitions Search for partial splits. –depth arg (=1) Depth at which to look for partial splits. –rooting arg (=0.9) Threshold in search for partial splits.
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <email@example.com>.
Benjamin Redelings. Feb 2018 trees-consensus(1)