trees-consensus - Find consensus trees and supported splits.

       Benjamin Redelings.

                                                    Feb 2018                                  trees-consensus(1)

       Find consensus trees and supported splits.

       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

-h, –help
              Produce help message.

       -V, –verbose
              Output more log messages on stderr.

       -sarg (=10%), –skiparg (=10%)
              Number of trees to skip.

       -uarg, –untilarg
              Read until this number of trees.

       -marg, –maxarg
              Thin tree samples down to this number of trees.

       -xarg (=1), –subsamplearg (=1)
              Factor by which to subsample.

       -iarg, –ignorearg
              Comma-separated list of taxa to ignore.

trees-consensus - Find consensus trees and supported splits.

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

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

–map-treesarg (=1)
              Only report the top arg trees per file.

       –min-supportarg (=0.25)
              Minimum threshold PP for splits.

       –reportarg
              Write supported partitions to file arg.

       –map-treearg
              Write out the map tree to file arg.

       –consensusarg
              Write out consensus trees.

       –greedy-consensusarg
              Write out greedy consensus trees.

       –extended-consensus-Larg
              Write out extended consensus trees + lengths.

       –extended-consensusarg
              Write out extended consensus trees.

       –support-levelsarg
              Write #branches versus LOD to file arg.

       –extended-support-levelsarg
              Write #sub-branches versus LOD to file arg.

–sub-partitions
              Search for partial splits.

       –deptharg (=1)
              Depth at which to look for partial splits.

       –rootingarg (=0.9)
              Threshold in search for partial splits.

       –odds-ratioarg (=1.5)
              Report partial-splits only if removing taxa improves the odds by at least this ratio.

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