micom-dev / micomLinks
Python package to study microbial communities using metabolic modeling.
☆104Updated last month
Alternatives and similar repositories for micom
Users that are interested in micom are comparing it to the libraries listed below
Sorting:
- CarveMe: genome-scale metabolic model reconstruction☆175Updated 3 months ago
- SMETANA: a tool to analyse interactions in microbial communities☆60Updated 2 months ago
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆82Updated 7 months ago
- Similarity networks of biosynthetic gene clusters☆119Updated last week
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆63Updated 5 months ago
- Pipeline for metabolic annotation of microbial genomes☆149Updated 3 months ago
- Find clustered hits from a BLAST search☆119Updated 7 months ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆28Updated 6 years ago
- ReFramed: metabolic modeling package☆59Updated 2 months ago
- memote – the genome-scale metabolic model test suite☆133Updated last year
- Systematic search of all known anti-phage systems.☆109Updated last month
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆181Updated 2 weeks ago
- Python package for building and analyzing models using ModelSEED☆23Updated 2 months ago
- Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…☆153Updated 2 months ago
- Bioinformatics program inStrain☆174Updated 2 months ago
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆242Updated 11 months ago
- motus - a tool for marker gene-based OTU (mOTU) profiling☆155Updated last year
- Download files from NCBI Entrez by accession☆126Updated 10 months ago
- MGnify genome analysis pipeline☆108Updated last week
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆21Updated 3 weeks ago
- antiSMASH☆215Updated 2 weeks ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆150Updated last month
- Materials and presentation for the 2023 ISB Microbiome course.☆24Updated 9 months ago
- MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.☆62Updated 7 months ago
- From annotated genomes to metabolic screening in large scale microbiotas☆62Updated 2 months ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆75Updated 2 years ago
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆18Updated 2 years ago
- Bioinformatics Tools☆87Updated 2 weeks ago
- scripts for predicting natural product activity from biosynthetic gene cluster sequences☆23Updated last month
- Neural networks for microbe-metabolite interaction analysis☆121Updated 2 years ago