The repository contains scripts to recreate the analyses presented in the manuscript, "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus" - https://peerj.com/articles/6142/

Scripts

mono.py - Computes the percentage of leaves that must be removed from a subtree to make it monophyletic. Included is the map of ids to genotypes (file Accession_GI_Genotype.csv). Usage: python mono.py -g <id_to_genotype> -t <input_tree> -o <output_file>  

consensus.pl - creates majority-rules consensus sequence (fasta format) from a fasta file containing multiple full genome sequences