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simple manipulation of trees

Project description

Build Status PyPI

smot - Simple Manipulation Of Trees

smot is a command line tool for manipulating, summarizing, and sampling from phylogenetic trees.


pip install smot


Python modules:

  • biopython
  • parsec
  • docopt

Python v3.6 and later (required for string interpolation)


Accessing usage information for each subcommand:

smot -h
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

# 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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