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acinetobacterplasmidtyping

agingclock

backblast_reciprocal_blast

This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.

bacterialgwas

A pipeline for performing genome-wide association tests for bacterial genomes.

bactopia

A flexible pipeline for complete analysis of bacterial genomes

biocode

Bioinformatics code libraries and scripts

bit

Bioinformatics Tools

cactus

Official home of genome aligner based upon notion of Cactus graphs

cart-python

python implementation of the CART algorithm

circlator

A tool to circularize genome assemblies

clinker

Gene cluster comparison figure generator

clusterdbanalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

compgen2021

dnds

A perl script to calculate dN/dS in batch based on Nei-Gojobori Method (the same as MEGA)

drep

Rapid comparison and dereplication of genomes

embl_gems

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

enrichkit

An R package performs over-representation test in multiple biological/annotation databases.

enveomics

Scripts and reference libraries at Kostas lab.

eukprot

Helper Perl scripts and tree files associated with the EukProt database of genome-scale eukaryotic protein sequence data sets.

fastani

Fast Whole-Genome Similarity (ANI) Estimation

gccalc

Calculate circos format data of GC content and GC skew from genome data.

genelab_data_processing

ggdc-robot

Automatically submit jobs to the Genome-to-Genome Distance Calculator (GGDC) website.

goatools

Python library to handle Gene Ontology (GO) terms

groves

Tools for analyzing trees

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

hisat2_featurecounts_mrna_seq

Make based mRNA-seq pipeline (QC, HISAT2, featureCounts). This is a gene level workflow for Single-End Illumina reads.

ifeature

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates fi

ifeatureomega-gui

iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versio

intarna

Efficient target prediction incorporating accessibility of interaction sites