Alternatives and similar repositories for CoMiDA

Users that are interested in CoMiDA are comparing it to the libraries listed below

• micom-dev / micom
  Python package to study microbial communities using metabolic modeling.
  ☆113Updated last week
• smirarab / sepp
  Ensemble of HMM methods (SEPP, TIPP, UPP)
  ☆95Updated 4 months ago
• cdanielmachado / embl_gems
  EMBL GEMs: A collection of GEnome-scale Models for bacterial species
  ☆30Updated 6 years ago
• biologyguy / BuddySuite
  Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
  ☆129Updated 4 years ago
• SystemsBioinformatics / cbmpy
  CBMPy is a Python based platform for constraint based modelling and analysis.
  ☆19Updated last year
• smirarab / pasta
  PASTA (Practical Alignment using SATe and Transitivity)
  ☆95Updated 6 months ago
• cdanielmachado / smetana
  SMETANA: a tool to analyse interactions in microbial communities
  ☆65Updated 7 months ago
• jameshadfield / phandango
  an interactive viewer for populations of bacterial genomes linked by a phylogeny
  ☆129Updated last year
• cdanielmachado / reframed
  ReFramed: metabolic modeling package
  ☆62Updated 2 months ago
• biocore / biom-format
  The Biological Observation Matrix (BIOM) Format Project
  ☆95Updated last month
• ModelSEED / ModelSEEDDatabase
  This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…
  ☆64Updated last week
• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆84Updated 7 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆62Updated 6 years ago
• medema-group / bigslice
  A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data
  ☆90Updated 4 months ago
• morgannprice / PaperBLAST
  PaperBLAST: find papers about a protein or its homologs
  ☆48Updated last week
• qiita-spots / qiita
  Qiita - A multi-omics databasing effort
  ☆127Updated last week
• meringlab / FlashWeave.jl
  Inference of microbial interaction networks from large-scale heterogeneous abundance data
  ☆90Updated 2 months ago
• wu-lab-uva / AMPHORA2
  An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
  ☆35Updated 6 years ago
• pirovc / genome_updater
  genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…
  ☆161Updated 3 weeks ago
• epruesse / SINA
  SINA - Reference based multiple sequence alignment
  ☆41Updated 4 years ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆116Updated last year
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆79Updated 2 years ago
• Gibbons-Lab / isb_course_2023
  Materials and presentation for the 2023 ISB Microbiome course.
  ☆24Updated last year
• AuReMe / metage2metabo
  From annotated genomes to metabolic screening in large scale microbiotas
  ☆67Updated 6 months ago
• evogytis / baltic
  baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development…
  ☆114Updated last week
• jrjhealey / bioinfo-tools
  Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
  ☆62Updated 5 years ago
• kblin / ncbi-acc-download
  Download files from NCBI Entrez by accession
  ☆131Updated last year
• metageni / SUPER-FOCUS
  A tool for agile functional analysis of shotgun metagenomic data
  ☆25Updated last year
• mmundy42 / mackinac
  Mackinac: A bridge between ModelSEED and COBRApy
  ☆19Updated 7 years ago
• hallamlab / metapathways2
  MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
  ☆33Updated 10 years ago