simple manipulation of trees


License
MIT
Install
pip install smot==0.12.0

Documentation

Build Status PyPI

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