focal (1) trees-consensus.1.gz

Provided by: bali-phy_3.4.1+dfsg-2build1_amd64 bug

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.


       --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>.


AUTHORS
       Benjamin Redelings.

                                                    Feb 2018                                  trees-consensus(1)