Pysimony

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

Features

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

Project Activity

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License

GNU General Public License version 3.0 (GPLv3)

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Additional Project Details

Intended Audience

Education, Science/Research

User Interface

Command-line

Programming Language

Python

Related Categories

Python Bio-Informatics Software

Registered

2012-07-10

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