smot 0.7.0

simple manipulation of trees

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