Man page - trees-consensus(1)

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Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

trees-consensus

NAME
SYNOPSIS
DESCRIPTION
INPUT OPTIONS:
REPORTING OPTIONS:
SEARCH OPTIONS:
EXAMPLES:
REPORTING BUGS:
AUTHORS

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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 .

Please send bug reports to bali-phy-users@googlegroups.com .

AUTHORS

Benjamin Redelings.

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