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Pysimony

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A Pythonic Implementation of Parsimony Inference of Phylogeny

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Description

UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/

Given Python's beauty, I know that someday I will have to finish Pysimony.

A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python.

Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format.

As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming.

Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel

Pysimony Web Site

Features

  • Flawed parsimony calculator
  • Reads FASTA files (only ATGC)
  • Outputs tree in Newick format
  • Simple, single mode

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Additional Project Details

Intended Audience

Science/Research, Education

User Interface

Command-line

Programming Language

Python

Registered

2012-07-10

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