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meshclust

MeShClust: an intelligent tool for clustering DNA sequences

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

modules

Environment Modules: provides dynamic modification of a user's environment

neatfreq

NeatFreq/Automaton Reference-Free Coverage Reduction Distribution Package

omastandalone

OMA standalone repository

orthofinder

Phylogenetic orthology inference for comparative genomics

pftool

plumed2

Development version of plumed 2

proovread

PacBio hybrid error correction through iterative short read consensus

pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.

pyani

Python module for average nucleotide identity analyses

python-client

A python client to query TemplateFlow via pyBIDS

ragout

Chromosome-level scaffolding using multiple references

repeatscout

The RepeatScout 1.0.5, written by Pevzner et al., source code for browsing. The official release and more information are available at http://bix.ucsd.edu/repeatscout/

scoary

Pan-genome wide association studies

seer

sequence element (kmer) enrichment analysis

signalp-6.0

Multi-class signal peptide prediction and structure decoding model.

singularity-cli

streamlined singularity python client (spython) for singularity

souporcell

Clustering scRNAseq by genotypes

spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

sweed

Likelihood-based Selective Sweep Detection

taxo_rrna

Creation of taxonomy Berleley DB for Silva and Greengenes 16S databases

taxodb_ncbi

NCBI Taxonomy Database formater

transit

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

ubin-helperscripts

Software for manual curation of genomes from metagenomes