Archive

TOOLS

Evolutionary Analysis

HyPhy: Analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.

Phylogenetic Tree

RAxML: Phylogenetic Tree Construction (Maximum Likelihood).

RAxML-NG: Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.

SplitsTree: Compute Phylogenetic Networks.

FigTree: Tool to graphically view phylogenetic trees.

iTOL: Online tool for phylogenetic tree display and annotation.

Sequence Alignment

ViralMSA: Reference-guided multiple sequence alignment of viral genomes.

Aliview: Alignment viewer and editor

MAFFT: Tool to create multiple sequence alignment based on progressive alignment algorithm.

Mauve: Tool to create multiple sequence alignment based on progressive alignment and alignment display.

Taxonomy

FastANI: Computing whole-genome Average Nucleotide Identity (ANI).

Kostas_lab_ANI: Estimates the average nucleotide identity using both best hits (one-way ANI) and reciprocal best hits (two-way ANI) between two genomic datasets.

GGDC: In-silico DNA DNA Hybridization (DDH).

TYGS: Genome-based prokaryote Taxonomy.

pairsnp: Construct pairwise SNP distance matrices from multiple sequence alignments.

Genome Annotation

Prokka: Rapid prokaryotic genome annotation.

Pan Genome Pipeline

Roary: Calculates the pan genome and core genome.

Genome-wide association study (GWAS)

Scoary: Pan-genome wide association studies (Pan-GWAS).

SNP Analysis

Snippy: Finds SNPs between a haploid reference genome and sequence isolates.

snipit: summarise snps relative to your reference sequence.

Database

ncbi-blast+: Local database construction and retrieval.

Motif Finder

FIMO: Searches a set of sequences for occurrences of known motifs.

Molecular Docking and Visualization

AutoDock Tools: Set-up ligand and receptor for AutoDock docking.

AutoDock Vina: Protein-Ligand Docking.

PyMOL: Molecular visualization system.

Comparative genomics

OrthoVenn: Comparison and annotation of orthologous gene clusters.

Recombination

ClonalFrameML: Inference of recombination in bacterial genomes.

Gubbins: Recombination predictions in bacterial genomes.

Antimicrobial resistance and lineage prediction

Mykrobe: Prediction of Antimicrobial resistance and Lineage in Mycobacterium tuberculosis.

RD-Analyzer: In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex.

Mobile Genetic Elements (MGEs) Analysis

MobileElementFinder: Identify Mobile Genetic Elements (MGEs) in Bacterial Genome

PHAST (PHAge Search Tool): Identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids (Online).

ISEScan: Identify IS (Insertion Sequence) elements in genome.

Others

Miniconda: Package management system and environment management system.

InteractiVenn: Tool to create Venn diagrams.

create_env: Method for creating an environment in conda.

Django: Python based web framework

Utility Tools

Tmux: Terminal multiplexer

R-Base: R package for Linux & Conda.

Terminator: Open-source terminal emulator (run multiple terminals).

Vim: Text editor for terminal.

PIPELINES

Bisulfite-sequencing-data-analysis: Pipeline for analysis of bisulfite sequencing data.

SARS-CoV-2 RdRp Molecular Docking: Pipeline for molecular docking analysis of SARS-CoV-2 RNA dependent RNA polymerase.