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.
- -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.
AUTHORS¶
Benjamin Redelings.