Repositories list

• mcorr

  Public
  Inferring bacterial recombination rates from large-scale sequencing datasets.

  recombinationcorrelation

  Go

  •8•41•6•1•Updated Feb 25, 2023Feb 25, 2023

• viral-mcorr

  Public
  Using correlated substitutions to infer recombination rates in RNA viruses

  virusesrecombinationcoronavirus+ 1sars-cov-2

  Go

  •

  Apache License 2.0

  •1•17•0•0•Updated Jan 26, 2023Jan 26, 2023

• virus_alignment_example

  Public
  Example workflow for aligning viral genomes for use with viral-mcorr using sars-like coronaviruses

  Python

  •0•0•0•0•Updated Sep 15, 2022Sep 15, 2022

• viral-mcorr_sl-cov_examples

  Public
  Example workflows for using viral-mcorr to infer recombination rates for RNA viruses

  HTML

  •0•0•0•0•Updated Sep 15, 2022Sep 15, 2022

• ReferenceAlignmentGenerator

  Public
  Mapping reads to the reference genome to construct consensus genomes and generate alignments

  Go

  •1•2•0•0•Updated Sep 15, 2022Sep 15, 2022

• mcorr-clustering

  Public
  Hierarchical clustering using mcorr

  Go

  •0•0•0•0•Updated Oct 26, 2021Oct 26, 2021

• ecological-memory

  Public
  Mathematica

  •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

• PangenomeAlignmentGenerator

  Public
  Align SRAs to pangenome FASTA file generated by Roary

  Go

  •1•1•0•0•Updated Jun 25, 2021Jun 25, 2021

• Helicobacter_pylori_transformation_experiments

  Public
  An example for mcorr

  0•0•0•0•Updated Jun 12, 2018Jun 12, 2018

• Helicobacter_pylori_global_population

  Public
  An example for mcorr

  Python

  •1•0•1•0•Updated Jun 12, 2018Jun 12, 2018

• mcorr_examples

  Public
  Example data for mcorr

  Python

  •0•0•0•0•Updated Jun 11, 2018Jun 11, 2018

• popsimu

  Public
  A GO package for population simulation with horizontal gene transfer

  Go

  •

  MIT License

  •0•1•0•0•Updated Apr 2, 2018Apr 2, 2018

• AssemblyAlignmentGenerator

  Public
  Generating core-gene alignments from assemblies.

  Python

  •0•0•1•0•Updated Feb 9, 2018Feb 9, 2018

• go-misc

  Public
  Go

  •0•0•0•0•Updated Jan 26, 2018Jan 26, 2018

• ncbiftp

  Public
  Go

  •1•0•0•0•Updated Jan 2, 2018Jan 2, 2018

• biogo

  Public
  Go

  •1•0•0•0•Updated Jan 2, 2018Jan 2, 2018

• hts

  Public
  biogo high throughput sequencing repository

  Go

  •

  BSD 3-Clause "New" or "Revised" License

  •41•0•0•0•Updated Dec 21, 2017Dec 21, 2017

• bamfilter

  Public
  Bam file filter

  Go

  •0•0•0•0•Updated Jul 22, 2017Jul 22, 2017

• hgtlib

  Public
  forward population simulations with selection and recombination

  C

  •1•1•0•0•Updated Aug 22, 2016Aug 22, 2016