trees-consensus

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.