Susie Grigson

biofaster. How fast can you read fastq/gz/bgz?

phagefactor. Python

recommend_a_journal. An AI-based journal recommender for your papers

PHANOTATE-rs. A fast Rust reimplementation of PHANOTATE

PHI-scripts. Repository to save the scripts run for a paper.

phage-seq-pvg. Sequence-Level Pangenome Variation Graphs for Bacteriophages

ProteomeLM. ProteomeLM: A proteome-scale language model allowing fast prediction of protein-protein interactions and gene essentiality across taxa

LexicMap. LexicMap: efficient sequence alignment against millions of prokaryotic genomes

GenoPHI. Python package for phage-host interaction prediction

LAMBDA. Python

longstrain. LongStrain: Strain resolution of microbial genomes using long reads

FlashPPI. Linear-time prediction of proteome-scale microbial protein interactions

hafeZ. A tool for identifying active prophage elements through read mapping

Merizo. Fast and accurate protein domain segmentation using Invariant Point Attention

vclust. Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes

peft. 🤗 PEFT: State-of-the-art Parameter-Efficient Fine-Tuning.

BiRNA-BERT. Python

RiNALMo. RiboNucleic Acid (RNA) Language Model

RNAsselem. a Python package for descriptive analysis of RNA secondary structure elements in viral genomes

lightmotif. A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

infernal. RNA secondary structure/sequence profiles for homology search and alignment

ictv-mmseqs2-protein-database. Python

RdRpCATCH. A community effort to create a shared resource for HMM-based RdRp discovery

add_pyrodigal_rv_models. Repository with notebooks on how the RNA virus models for pyrodigal-rv were created and benchmarked.

pyrodigal-rv. A Pyrodigal extension to predict genes in RNA viruses.

Skadi. SKADI: Sequence-based Knowledgebase for Annotation, Detection, and Identification

VITAP. The viral taxonomic assignment pipeline

PholdAPhage. Assembling phage particles one protein at a time

agtools. 🛠️🧬 A Software Framework to Manipulate Assembly Graphs

hpci. Haskell

ggpubfigs. colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures

DiffDock-PP. Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)

tracs. Fast pairwise transmission inference from single genome and/or metagenomic data

megapharokka. A fork of Pharokka to handle enVhogs

pharokka. Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.

D-SCRIPT. A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions

GeoDock. Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

Cfold. Structure prediction of alternative protein conformations

viral-protein-function-plm. Viral protein family functional prediction using protein language models

atavide_lite. A simpler version of atavide that relies only on slurm or PBS scripts. Some of the settings are specific for our compute resources

ProstT5. Bilingual Language Model for Protein Sequence and Structure

ProtTrans. ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.