abaylyi-ee

Acinetobacter baylyi ADP1 evolution and engineering

avida-ptm

barricklab

General data analysis spreadsheets and scripts

barricklab_calendar

Google Calendar to Slack Daily Events

bioconda-recipes

Conda recipes for the bioconda channel.

bpopsim

Simulator of evolutionary dynamics in asexual populations. Tools for creating Muller plots to visualize these dynamics.

brefito

Snakemake pipelines for assembling and annotating bacterial reference sequences

breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.

breseq-ext-cnv

breseq copy number variation extension

breseq-ext-multisample

breseq-ext-paired-end

breseq extension for calling mutations from paired end read mapping

breseq-ext-specificity

breseq extension for analyzing the specificity of genome evolution in samples from different treatments

breseq-gui

Electron GUI for breseq

brnaseq

Basic analysis of bacterial RNAseq data for differential gene expression

btk

Broad-host-range Toolkit (BTK) for genetic engineering of non-model bacterial species

burden

Burden monitor related scripts

cryptkeeper

Tool for visualizing unintentional bacterial gene expression from a DNA sequence

efm-analysis

Code for analyzing sequencing data from Freshman Research Initiative genetic failure mode experiments

efm-calculator

Evolutionary Failure Mode Calculator

efm-calculator-2

Evolutionary Failure Mode Calculator v2

fitnessr

R package for calculating relative fitness from co-culture competition assays

fraggenescan

fugues

Protocols for Functional Genomics using Engineered Symbionts (FUGUES)

genomediff-python

GenomeDiff (*.gd) file parser for Python

homebrew-science

:beer::microscope: Scientific formulae for the Homebrew package manager

igem2019

Scripts and datasets for measuring BioBrick plasmid burden.

igem2020

University of Texas at Austin 2020 iGEM Team

igem2021

ltee-ecoli

Genomics resources for the Long-Term Evolution Experiment with E. coli

ltee-metagenomic

Time-resolved metagenomic sequencing of Lenski's long-term evolution experiment with Escherichia coli