| layout | page |
|---|---|
| title | Software |
| permalink | /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
- LAFA The Longitudinal Assessment of Protein Function Annotaton server continuously assesses protein function prediction models. The models are containerized and run on periodically updated benchmarks of protein function annotations compiled from several sources.
- GOThresher Use this to remove annotation biases from Uniprot-GOA files. Usefule for preparing training 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.