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.
-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.
--ignore arg
Comma-separated list of taxa to ignore.

REPORTING OPTIONS:

--map-trees arg (=1)
Only report the top trees per file.
--map-tree arg
Write out the map tree to file .
--min-support arg (=0.25)
Minimum threshold PP for splits.
--report arg
Write supported partitions to file .
--consensus-PP arg
Write out consensus trees+PP.
--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 .
--extended-support-levels arg
Write #sub-branches versus LOD to file .
--odds-ratio arg (=1.5)
Report partial-splits only if removing taxa improves the odds by at least this ratio.
-v, --verbose
Output more log messages on stderr.

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.

REPORTING BUGS:

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

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