SystemsBioinformatics / ecmtoolLinks
Uncover organisms' metabolic blueprints
☆13Updated last year
Alternatives and similar repositories for ecmtool
Users that are interested in ecmtool are comparing it to the libraries listed below
Sorting:
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆23Updated 2 months ago
- From annotated genomes to metabolic screening in large scale microbiotas☆68Updated 3 weeks ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆30Updated 6 years ago
- SMETANA: a tool to analyse interactions in microbial communities☆66Updated 9 months ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆14Updated 2 years ago
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆65Updated last month
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆95Updated 5 months ago
- ☆43Updated 7 months ago
- ☆14Updated 2 months ago
- MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.☆72Updated last month
- CarveMe: genome-scale metabolic model reconstruction☆194Updated 4 months ago
- Detection of phage RBPs based on protein domains and machine learning☆30Updated last year
- Python package to study microbial communities using metabolic modeling.☆115Updated last week
- Pipelines used in the lab.☆15Updated 10 months ago
- ☆50Updated last month
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆76Updated 9 months ago
- PHANOTATE: a gene caller for phages.☆82Updated last year
- A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes☆49Updated 2 years ago
- Systematic search of all known anti-phage systems.☆144Updated 2 weeks ago
- Predict the function of phage hypothetical proteins using an LSTM model trained with Phage Synteny☆58Updated 8 months ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆176Updated 3 weeks ago
- Supporting code for uncultivated gut virus manuscript☆78Updated 2 years ago
- lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters☆41Updated 4 months ago
- Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome☆67Updated 10 months ago
- PhaTYP: Predicting lifestyle for bacteriophages using BERT☆15Updated last year
- Phage Annotation using Protein Structures☆148Updated this week
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins☆15Updated 4 years ago
- Viral protein family functional prediction using protein language models☆21Updated last month
- ☆14Updated last week
- Binning Virus Genomes from Metagenomes☆70Updated 3 years ago