DOKK / manpages / debian 12 / bali-phy / trees-consensus.1.en
trees-consensus(1) trees-consensus(1)

trees-consensus - Find consensus trees and supported splits.

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

Find consensus trees and supported splits.

Produce help message.
Output more log messages on stderr.
Number of trees to skip.
Read until this number of trees.
Thin tree samples down to this number of trees.
Factor by which to subsample.
Comma-separated list of taxa to ignore.

Only report the top arg trees per file.
Minimum threshold PP for splits.
Write supported partitions to file arg.
Write out the map tree to file arg.
Write out consensus trees.
Write out greedy consensus trees.
Write out extended consensus trees + lengths.
Write out extended consensus trees.
Write #branches versus LOD to file arg.
Write #sub-branches versus LOD to file arg.

Search for partial splits.
Depth at which to look for partial splits.
Threshold in search for partial splits.
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:

% 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
    

BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

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

Benjamin Redelings.

Feb 2018