trees-consensus(1)

Usage

trees-consensus [OPTIONS] sampled-trees [sampled-trees ... sampled-trees]

Find consensus trees and supported splits.

`-h, –help`	Produce help message.
`-V, –verbose`	Output more log messages on stderr.
`-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.
`-i arg, –ignore arg`	Comma-separated list of taxa to ignore.

`–map-trees arg (=1)`	Only report the top arg trees per file.
`–min-support arg (=0.25)`	Minimum threshold PP for splits.
`–report arg`	Write supported partitions to file arg.
`–map-tree arg`	Write out the map tree to file arg.
`–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 arg.
`–extended-support-levels arg`	Write #sub-branches versus LOD to file arg.

–odds-ratio arg (=1.5): Report partial-splits only if removing taxa improves the odds by at least this ratio.

Compute the majority consensus tree, skipping the first 10% of trees:

: % trees-consensus newick.trees > c50.tree % trees-consensus newick.trees --skip=10% > c50.tree

Skip the first 100 trees:

Skip the first 20% of trees and take every 10th tree thereafter:

Compute the 50% (majority) and 80% consensus trees:

: % trees-consensus newick.trees --consensus=0.5:c50.tree,0.8:c80.tree % trees-consensus newick.trees --consensus=0.5,0.8:c80.tree > c50.tree

Compute the MAP tree and write a summary of supported partitions:

Compute the MAP tree and write it to the standard output:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .

4 releases since Debian 10 (Buster); the text changed 2 times.