Software

SwiftOrtho SwiftOrtho is a fast orthology analysis tool that identifies orthologs, paralogs, and co-orthologs for genomes using a graph-based approach.
ROAGUE (Reconstruction of Ancestral Gene Blocks Using Events) is a tool to reconstruct ancestors of gene blocks in prokaryotic genomes. Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed.
POEM POEM is a pipeline that can predict operons and core operons from metagenomic genome/assembly or short reads. It can be run on most * NIX systems.
TreasureIsland TreasureIsland is a machine learning-based Genomic Island prediction software that uses an unsupervised representation of DNA for its prediction.
EpicTope Epitope tagging is a technique enabling the identification, tracking, and purification of proteins in vivo. EpicTope helps experimentalists identify proter epitope insertion sites using CRISPR-cas9

GOThresher Use this to remove annotation biases from Uniprot-GOA files. Usefule fro preparing rtaining sets for protein function prediction software.
CAFA_Benchmark Create benchmarks fro CAFA assessments using Uniprot-GOA files from different dates.
CAFA-swissprot create an initial dataset for CAFA competitors from a Swissprot-Uniprot file.
CAFA_evaluation a suite of tools to evaluate CAFA predictions.

paperchaser A script that accepts a file of author names and prints out the collective papers of these authors. No duplicaitons, i.e. of two or more authors collaborated on a paper, that paper will appear only once. The script uses Biopython’s Entrez utilities to get the papers from the PubMed database. Other manuscript repositories are not supported currently.
authorator A Python program to create a LaTeX file with a large number of authors and affiliations.