Software
Open-source bioinformatics tools developed by the Creevey Lab
We are committed to open science. All tools are freely available and published with peer-reviewed methodology. If you use any of our software, please cite the relevant publication.
Amply
A computational pipeline for identifying novel Antimicrobial Peptides (AMPs) from any form of digital biological data, for synthesis and screening against multi-drug resistant bacteria and fungi.
Apply Decision Tree
A tool for easy implementation of j48 decision trees from WEKA on novel datasets, developed to streamline machine learning workflows in bioinformatics.
AQUA
Automated Quality Improvement for multiple sequence alignments. Automatically identifies the most reliable alignment for a given protein family using MUSCLE, MAFFT, RASCAL, and NORMD.
CatSequences
A tool for concatenating multiple FASTA alignments for supermatrix phylogenetic analyses, part of a general phylogenomics software suite.
Clann
Construction of supertrees and exploration of phylogenomic information from partially overlapping datasets. Implements optimal phylogenetic supertree methods.
Clan Check
Analyses single-copy phylogenetic trees to assess compatibility with user-defined groupings (clans) in unrooted trees — ideal for large-scale phylogenomic analyses.
Concatabominations
Identifies unstable taxa in morphological phylogenetics using a heuristic extension to Safe Taxonomic Reduction, with Cytoscape-based visualisation of taxonomic equivalents.
CowPI
A rumen microbiome-focused version of the PICRUSt functional inference software, built using 16S rDNA profiles from the Global Rumen Census and ~500 fully sequenced microbial genomes.
Crann
Detects adaptive evolution in protein-coding genes. Implements methods for measuring synonymous/non-synonymous distances and detecting directional and non-directional positive selection.
Hansel & Gretel
Twin tools for identifying cryptic haplotypes from metagenomic datasets. Hansel implements a graph-inspired data structure; Gretel recovers haplotypes from metagenomes.
Machete
Automated likelihood decay indices and maximum likelihood phylogeny construction with PAUP*. Takes nexus-formatted aligned sequences and optimises ML trees and bootstrap analyses.
MGKit
A metagenomic framework for the study of microbial communities, providing fully automated analysis from NGS reads to assembly, gene prediction, taxonomic identification, and SNP diversity estimation.
SNPdat
Software for annotation of novel and known single nucleotide polymorphisms (SNPs), designed for organisms with limited SNP annotation or those not supported by other tools.
Spherical
An iterative approach to assembling large metagenomic datasets. Produces more complete assemblies from deep-sequenced data while using a fraction of the RAM otherwise required.
StORF-Reporter
A toolkit that takes an annotated genome and returns missed CDS genes from unannotated regions, outputting results in PROKKA-formatted GFF files.
Treedist
Rapid calculation of pathlength distances between taxa on phylogenetic trees. Includes treedist_pair (distance between two branches) and treedist_all (all terminal branch distances).