Software

POUTINE

A homoplasy-counting-based method for genome-wide association studies (GWAS).

Get the code and documentation.

Reference:
Chen P & Shapiro BJ (2021) bioRxiv.

BacGWASim
​
​A simulator of bacterial genomes and phenotypes to benchmark genome-wide association studies

Get the code and documentation.

Reference:
Saber MM & Shapiro BJ (2020) Microbial Genomics.

symsim

Symsim is a simple simulation of sympatric speciation in recombining microbial populations.

Get the code and documentation.

Reference:
Friedman J, Alm EJ, Shapiro BJ. (2013) PLOS ONE

STARRInIGHTS
Strain-based Tree Analysis and Recombinant Region Inference In Genomes from High-Throughput Sequencing projects

Get the code and documentation.

Reference:
Shapiro BJ et al. (2012) Science.

  
  Miscellany

sciku

A collection of illustrated science poetry.
www.sciku.org