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    52 repositories

    • breseq

      Public
      breseq is a computational pipeline for finding mutations relative to a reference sequence using high-throughput DNA resequencing data. It is intended for haploi…
      C++
      •
      GNU General Public License v2.0
      •23•204•34•0•Updated Jun 7, 2026Jun 7, 2026

    • cryptkeeper

      Public
      Tool for visualizing unintentional bacterial gene expression from a DNA sequence
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated May 28, 2026May 28, 2026

    • pLannotate

      Public
      Webserver and command line tool for annotating engineered plasmids
      Python
      •
      GNU General Public License v3.0
      •33•17•0•0•Updated May 19, 2026May 19, 2026

    • LTEE-Ecoli

      Public
      Genomics resources for the Long-Term Evolution Experiment with E. coli
      GAP
      •
      Creative Commons Zero v1.0 Universal
      •5•19•1•0•Updated May 18, 2026May 18, 2026

    • seabreeze

      Public
      seabreeze: A Pipeline for Analyzing Structural Variation Between Bacterial Genome Assemblies
      bioinformatics-pipelinestructural-variationlong-read-sequencing
      bioinformatics-pipelinestructural-variationlong-read-sequencingexperimental-evolution
      Python
      •
      MIT License
      •2•4•7•0•Updated May 12, 2026May 12, 2026

    • teachPress

      Public
      Fork of teachPress (course and publication management plugin for WordPress) with some customizations
      PHP
      •
      GNU General Public License v2.0
      •44•0•0•0•Updated May 3, 2026May 3, 2026

    • brefito

      Public
      Snakemake pipelines for analyzing resequenced bacterial genomes
      Python
      •
      MIT License
      •1•3•0•0•Updated Apr 30, 2026Apr 30, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •4k•0•0•0•Updated Apr 25, 2026Apr 25, 2026

    • barricklab

      Public
      General data analysis spreadsheets and scripts
      Python
      •3•4•0•0•Updated Apr 24, 2026Apr 24, 2026

    • CNery

      Public
      breseq copy number variation extension
      Python
      •
      GNU General Public License v2.0
      •0•0•1•0•Updated Apr 21, 2026Apr 21, 2026

    • Ecoli-phage-ssrs

      Public
      Analysis of simple sequence repeats in E. coli bacteriophage genomes that may act as contingency loci
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • LTEE-leaderboard

      Public
      Shiny tool for viewing the transfer history of the E. coli Long-Term Evolution Experiment
      R
      •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • efmcalculator2

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Oct 27, 2025Oct 27, 2025

    • barricklab_calendar

      Public
      Google Calendar to Slack Daily Events
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • phlame

      Public
      Python
      •
      MIT License
      •6•0•0•0•Updated Aug 15, 2025Aug 15, 2025

    • ostir

      Public
      Software for predicting translation initiation rates in bacteria
      synthetic-biologyrna-structurebioengineering
      synthetic-biologyrna-structurebioengineering
      Python
      •
      GNU General Public License v3.0
      •9•33•3•0•Updated Jul 30, 2025Jul 30, 2025

    • ltee-sv-seabreeze

      Public
      Modified version of seabreeze for analysis of LTEE data
      Python
      •
      MIT License
      •2•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • genomediff-python

      Public
      GenomeDiff (*.gd) file parser for Python
      Python
      •
      MIT License
      •5•0•0•1•Updated Feb 11, 2025Feb 11, 2025

    • RhoTermPredict

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •11•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • promoter-calculator

      Public
      Python
      •
      Other
      •0•6•0•0•Updated Aug 8, 2024Aug 8, 2024

    • igem2019

      Public
      Scripts and datasets for measuring BioBrick plasmid burden.
      R
      •1•1•0•0•Updated Jul 17, 2024Jul 17, 2024

    • ND-Bartonella-EE

      Public
      Code for analyzing mutations that evolved in Bartonella bacteria passaged through rodents in the laboratory.
      GDScript
      •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

    • ND-Bartonella-SSR

      Public
      R
      •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

    • breseq-gui

      Public
      Electron GUI for breseq
      JavaScript
      •
      MIT License
      •1•4•0•7•Updated Sep 6, 2023Sep 6, 2023

    • fitnessR

      Public
      R package for calculating relative fitness from co-culture competition assays
      HTML
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 21, 2023Apr 21, 2023

    • widespread-recurrent-part-variants

      Public
      Analysis code for identifying genetic part variants in engineered plasmids
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 20, 2023Apr 20, 2023

    • FragGeneScan

      Public
      C
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Aug 1, 2022Aug 1, 2022

    • Abaylyi-EE

      Public
      Acinetobacter baylyi ADP1 evolution and engineering
      GDScript
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Jun 3, 2022Jun 3, 2022

    • efm-calculator

      Public
      Evolutionary Failure Mode Calculator
      Python
      •
      Other
      •1•3•0•0•Updated Mar 20, 2022Mar 20, 2022

    • brnaseq

      Public
      Basic analysis of bacterial RNAseq data for differential gene expression
      Perl
      •
      MIT License
      •0•3•0•0•Updated Oct 15, 2021Oct 15, 2021
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