Software

Panaroo

An error aware pipeline for pangenome investigation

Fastbaps

Fastbaps is a fast solution to the genetic clustering problem. It rapidly identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach clusters datasets 10–100 times larger than the existing model-based methods.

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Panstripe

Robust analysis of prokaryotic pangenome gene gain and loss rates

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LDWeaver

Led by Sudaraka, LDWeaver is a highly scalable algorithm for detecting evidence of co-selection and epistasis in bacterial genomes.

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Pairsnp

Pairsnp is used to quickly obtain pairwise SNP distance matrices from multiple sequence alignments. For larger alignments, pairsnp is an order of magnitude faster than approaches based on pairwise comparison of every site.

Code

RhierBAPS

An R implementation of hierBAPS, a popular algorithm for identifying population structure in haploid genomes.

Code Manuscript