Folder structure: doc folder: project report and notebook source folder: running scripts bin folder: supporting programs results: inside each subfolder are SQLite database and logs for each running time. data: testing data Project requirement: Python 2.7 Biopython 1.6 SQLite 3 Project environment: Unix To remove noisy column from one MSA file, use this command: ./reducenoise.py -in inputFile -out outputFile both inputFile and outputFile are Fasta format To evaluate the constructed tree from denoised MSA files in a folder, use this command: ./evaluate -dir folderName this command will write all distances and corresponding file name to stdout To stores the calculated distances, use this command: ./updateSQL.py -in statisticInput -out sqliteFile this script takes the output of the evaluate command as its input, all the distances will then be stored in SQLite database To execute all above steps with all provided data use runall script inside source folder. This script will create a subfolder in side results folder that corresponded to the running time (format: yyyymmddhhmm)