Metadata-Version: 2.1
Name: smot
Version: 0.6.0
Summary: simple manipulation of trees
Home-page: https://github.com/flu-crew/smot
Author: Zebulun Arendsee
Author-email: zebulun.arendsee@usda.gov
License: UNKNOWN
Description: [![Build Status](https://travis-ci.org/flu-crew/smot.svg?branch=master)](https://travis-ci.org/flu-crew/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.
        
        
         | 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
        
        ``` 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
        ```
        
        
        ![](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
