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

See All Activity >

Categories

Bio-Informatics

License

GNU General Public License version 3.0 (GPLv3)

Follow Pysimony

Pysimony Web Site

Other Useful Business Software
Gen AI apps are built with MongoDB Atlas Icon
Gen AI apps are built with MongoDB Atlas

Build gen AI apps with an all-in-one modern database: MongoDB Atlas

MongoDB Atlas provides built-in vector search and a flexible document model so developers can build, scale, and run gen AI apps without stitching together multiple databases. From LLM integration to semantic search, Atlas simplifies your AI architecture—and it’s free to get started.
Start Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of Pysimony!

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