Metadata-Version: 2.1
Name: smot
Version: 0.3.0
Summary: simple manipulation of trees
Home-page: https://github.com/arendsee/smot
Author: Zebulun Arendsee
Author-email: zbwrnz@gmail.com
License: UNKNOWN
Description: [![Build Status](https://travis-ci.org/arendsee/smot.svg?branch=master)](https://travis-ci.org/arendsee/smot)
        ![PyPI](https://img.shields.io/pypi/v/smot.svg)
        
        # smot - Simple Manipulation Of Trees
        
        `smot` is a command line tool for manipulating, summarizing, and sampling from
        phylogenetic trees.
        
        ## Installation
        
        ``` sh
        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:
        
        ``` sh
        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 |
        
        
        ![](images/pdm-1.png)
        
        ``` sh
        # 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
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
