parsimony_scorer

Parsimony_Scorer takes in a file of newick-format strings and a nexus file of data. It then builds and scores the given evolutionary trees, finding the most parsimonious tree according to the given data set.

The test data and function runs all possible rooted trees with 6 leaves on 3 datasets from separate nexus files.

DEPENDENCIES:

• This code uses Biopython and numpy

NOTES:

• Parsimony_Tree expects your newick strings to have spaces after commas. You have to manually update what's inside the .split() method on line 32 if you want to remove them
• Parsimony_Scorer expects your newick file to have each tree on its own line
• Put any nexus files you use in the nexus_files folder, or manually remove "nexus_files/"+ from line 18 of parsimony_scorer.py
• If the names you use in your newick file don't match the names you use in your nexus files, send update_taxa_names in Parsimony_Scorer a list of names as they appear in the newick file before calling run. Make sure that the list is in the same order as they appear in the nexus file.
• If more than one tree shares the best score, the code will not always return the same one. This is because the score-tree pairs are stored in a dictionary (scored_trees), which is ordered differently each time.
• rooted_trees.txt holds all viable permutations of a rooted 6-taxa tree. It and its 'named' counterpart are for testing the Parsimony_Scorer used in congruence with the nexus files already in the nexus_files folder