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