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COBRApy is a package for constraint-based modeling of metabolic networks.
Assessing the quality of metagenome-derived genome bins using machine learning
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
High-quality circular representations of taxonomic and phylogenetic trees
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
Virus Identification By iteRative ANnoTation
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
customizable pipeline to identify viral sequences from (meta)genomic data
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
A tool for identifying phages and plasmids from metagenomic fragments using deep learning
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
A game theoretic approach to explain the output of any machine learning model.
The second version of the Kraken taxonomic sequence classification system
Phylogenetic orthology inference for comparative genomics
The LucaOne’s code, including model code and pre-training code.
This package contains deep learning models and related scripts for RoseTTAFold
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
MMseqs2: ultra fast and sensitive search and clustering suite
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Identifying viruses from metagenomic data by deep learning
Repository for StripedHyena, a state-of-the-art beyond Transformer architecture
Biological foundation modeling from molecular to genome scale
A versatile pairwise aligner for genomic and spliced nucleotide sequences
De novo assembler for single molecule sequencing reads using repeat graphs