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trees-consensus(1) trees-consensus(1)

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.
Feb 2018