This file contains brief explanations for files in this repository. For more explanation on how to run a script look at comment block on top of each file To compile the project: > make To run the neighbor-joining algorithm: > ./main <INPUT> <OUTPUT> <VERBOSE> where INPUT: file containing protein names and a distance matrix (see data/*.dist files to the format) OUTPUT: file to store the computed phylogenetic tree VERBOSE: type "verbose" to print debugging logs Source Files: ---------------------aligntodist_pw.pl------------------- This script creates distance matrixes using pairwise global alignment scores ---------------------pairwisealignment.sh---------------- This script creates pair alignments ---------------------aligntodist.pl---------------------- This script creates distance matrixes using distmat program from emboss package ---------------------fasta_parser.sh--------------------- This is a helper script used to create .fasta files for each protein sequence ---------------------experiments.pl---------------------- This script runs the experiment conducted in this project. It takes one argument; 1, 2, or 3 # input: 1,2,3; 1 to run distmat expriment, # 2 to run pairwise global score experiment, # and 3 to run protdist experiment ---------------------compareTrees.py---------------------- This converts output tree of our NJ implementation into newick format # and also generates the accuracy score for given two phylogenetic trees ---------------------makefile--------------------- Creates executables ---------------------joiner.h--------------------- Header file of joiner.cpp ---------------------joiner.cpp--------------------- This file contains main Neighbor-Joining algorithm ---------------------main.cpp--------------------- Main source file of Neighbor-Joining implementation ---------------------protdist.c--------------------- This is the modified version of phylib's protdist program. It is only used in experiment.pl script. ---------------------phylip.c--------------------- A library from phylib ---------------------phylip.h--------------------- A header from phylib -------------------------------------------------- Binaries: ---------------------main------------------------- main.c executable ---------------------protdist--------------------- protdist. c executable Other files: ---------------------infile----------------------- It is the same as 85VAST.aln but only in a different format. it is used in protdist experiment. ---------------------README----------------------- This file Directories: ---------------------data------------------------- Contains all data used in and produced by this project ---------------------report----------------------- Contains the source of final report Dependicies: Inorder to run the experiment of this project following software should be installed: emboss, phylib python libraries: ete2, networkx perl libraries: Time::HiRes NOTE: there are some hard coded directory path in the code! They are generally mentioned in the comments on top of each file.