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                          trees-consensus(1)