NAME
trees-consensus - Find consensus trees and supported splits.
SYNOPSIS
trees-consensus [OPTIONS] sampled-trees [sampled-trees ... sampled-trees]
DESCRIPTION
Find consensus trees and supported splits.
INPUT OPTIONS:
- -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.
REPORTING OPTIONS:
- –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.
SEARCH OPTIONS:
- –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.
- –odds-ratio arg (=1.5)
-
Report partial-splits only if removing taxa improves the odds by at least this ratio.
EXAMPLES:
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:
-
% trees-consensus newick.trees --skip=100 > c50.tree
Skip the first 20% of trees and take every 10th tree thereafter:
-
% trees-consensus newick.trees --skip=20% -x10 > c50.tree
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:
-
% trees-consensus --map-tree=MAP.tree --report=partitions.txt
Compute the MAP tree and write it to the standard output:
-
% trees-consensus --map-tree=- --report=partitions.txt
REPORTING BUGS:
BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.