This repository contains all data for CSC525 project.

Abricate_HolobeeResults_NCBI_AMRFinderPlus.txt

This file contains the output from abricate that searches the Holobee-Mop database against the NCBI AMRFinderPlus database.

Holobee_ARGs_gene_regions.fasta

This file contains the fasta files of the gene regions of the species matching the ARGs found in the ABRicate search results in Abricate_HolobeeResults_NCBI_AMRFinderPlus.txt

Abricate_on_Megahit_contigs.txt

This file contains the ABRicate search results of the contigs assembled by MEGAHit against the NCBI AMRFinderPlus database.

Abricate_on_discarded_contigs.txt

This file contains the ABRicate search results of the contigs discarded by Metabat against the NCBI AMRFinderPlus database.

Abricate_on_Metabat_bins.txt

This file contains the ABRicate search results of the bins from Metabat against the NCBI AMRFinderPlus database.

The following files contain the multiple sequence alignments created from the four tools used for guide tree/phylogenetic trees

MAAFT: Holobee_ARGs_CLUSTAL_format_alignment_by_MAFFT (v7.490).txt

T-Coffee: T-coffee-multiple sequence alignment.txt

webPRANK: webprank_SA.txt

Clustal Omega : Clustal_Omega_MSA.txt

MSA_guide_trees.xlsx

Contains the guide Trees for each tool