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.
- -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.
- --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 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 <email@example.com>.