simple manipulation of trees
Project description
smot - Simple Manipulation Of Trees
smot
is a command line tool for manipulating, summarizing, and sampling from
phylogenetic trees.
subcommand | description |
---|---|
convert | convert tree format |
tips | list tip labels |
plot | plot the tree |
sample | sub-sample a tree |
factor | integrate and/or infer classes for tips |
tipsed | regex-based search and replace across tip labels |
midpoint | root tree by midpoint |
random | make random tree given list of tip labels |
clean | remove singleton nodes and ladderize |
Installation
pip install smot
Requirements
Python modules:
- biopython
- parsec
- docopt
Python v3.6 and later (required for string interpolation)
Examples
Accessing usage information for each subcommand:
smot -h
# image B
smot sample equal --factor-by-capture="(human|swine)" --keep="swine" --seed=42 --max-tips=2 pdm.tre > pdm-equal.tre
# image C
smot sample prop --proportion=0.1 --min-tips=2 --factor-by-capture="(human|swine)" --keep="swine" --seed=42 pdm.tre > pdm-prop.tre
# image D
smot sample para --proportion=0.1 --min-tips=2 --factor-by-capture="(human|swine)" --keep="swine" --seed=42 pdm.tre > pdm-para.tre
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