micom-dev / micom
Python package to study microbial communities using metabolic modeling.
☆97Updated 2 weeks ago
Alternatives and similar repositories for micom:
Users that are interested in micom are comparing it to the libraries listed below
- CarveMe: genome-scale metabolic model reconstruction☆164Updated 5 months ago
- SMETANA: a tool to analyse interactions in microbial communities☆58Updated 4 years ago
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆78Updated 3 months ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆25Updated 5 years ago
- Pipeline for metabolic annotation of microbial genomes☆142Updated 7 months ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆19Updated 9 months ago
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆59Updated 2 weeks ago
- Similarity networks of biosynthetic gene clusters☆97Updated this week
- Find clustered hits from a BLAST search☆111Updated 2 months ago
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆17Updated 2 years ago
- memote – the genome-scale metabolic model test suite☆130Updated last year
- ReFramed: metabolic modeling package☆57Updated 6 months ago
- From annotated genomes to metabolic screening in large scale microbiotas☆54Updated 5 months ago
- Python package for building and analyzing models using ModelSEED☆22Updated 2 months ago
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆16Updated 3 weeks ago
- MGnify genome analysis pipeline☆104Updated this week
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆174Updated last week
- Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models☆12Updated last year
- Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for…☆150Updated 3 weeks ago
- Phage Annotation using Protein Structures☆96Updated last week
- GenoVi, an automated customizable circular genome visualizer for bacteria and archaea☆86Updated last year
- A tool for representing genomic potential and transcriptomic expression into KEGG pathways☆53Updated 6 months ago
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆67Updated last month
- CCTyper: Automatic detection and subtyping of CRISPR-Cas operons☆99Updated last year
- Download files from NCBI Entrez by accession☆119Updated 5 months ago
- MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.☆57Updated 2 months ago
- Systematic search of all known anti-phage systems.☆88Updated 2 weeks ago
- Bioinformatics tool for Locus Visualisation☆85Updated 2 weeks ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆71Updated last year
- Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome☆44Updated last month