Increasing Biogeographical Resolution

INSTRUCTIONS

Run the following command:

Python.exe Pipeline.py .txt .txt .fasta

The pipeline requires four arguments: inputFile - the name/path of the ISG data file outputFile - the name/path used to create the output files treeFile - the name/path of the phylogenetic tree file referenceFile - the name/path of the FASTA file used as the reference genome in the ISG data

The pipeline creates two files, .txt and .fasta, which will be saved into the currently open directory by default, or in the directory indicated by the outputFile path. .txt contains all the sequences and the genomes/groups that they differentiate in a human-readable format. .fasta contains all the sequences in FASTA format.