flass

canu

A single molecule sequence assembler for genomes large and small.

GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

biosql

GeneRax

pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

hamburger

HMmer Based UndeRstandinG of gene clustERs

twilight

All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis

didehpc

:cloud::computer::cloud: Support for the DIDE cluster

sling

a tool to search for linked gene arrays in bacterial datasets

BaGPipe

A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge

BacQuerya-processing

Scripts to process publicly available information for indexing.