gtonkinhill

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Peter MacCallum Cancer Centre & University of Melbourne

Australia

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UniMelb-Day-Lab

Gerry Tonkin-Hill's repositories

panaroo

An updated pipeline for pangenome investigation

Language:PythonMIT240 12 253

fastbaps

A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data

Language:RMIT55 6 25

panstripe

post processing of bacterial pangenome gene presence/absence matrices

Language:RGPL-2.043 2 13

pairsnp

A set of scripts for calculating pairwise SNP distance

MIT34 6 6

TCGA_analysis

Language:HTML25 3 2

tracm

Fast pairwise transmission inference from single genome and/or metagenomic data

Language:Python12 4 2

pairsnp-cpp

Fast pairwise SNP distance matrices from Multiple Sequence Alignments

Language:C++MIT4 20

SC2_withinhost

Language:HTML4 4 1

fasttranscluster

Language:Python3 4 5

pneumo_withinhost_manuscript

Language:HTML2 30

troms-_workshop

Language:HTML2 20

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonMIT100

genesearch

Language:Python1 30

gtonkinhill.github.io

Language:HTML1 2 1

mandrake-web

Language:C++MIT1 20

TransPhylo_mod

Language:R1 50

Assembly-Dereplicator

A tool for removing redundant genomes from a set of assemblies

Language:PythonGPL-3.0000

bioconda-recipes

Conda recipes for the bioconda channel.

Language:ShellMIT010

ffpopsim

FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

Language:C++GPL-3.0020

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Language:PythonGPL-2.0010

labsite

Language:HTML010

Magphi

Tool intended to pull out sequences and annotations between insertion sites specified by the user.

Language:PythonMIT010

mandrake_manuscript

Language:HTML040

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Language:PythonMIT000

MutTui

MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets

Language:PythonMIT010

muttui_test_data

020

panstripe-manuscript

Language:HTML020

relate

Software for estimating genome-wide genealogies for thousands of samples

Language:C++NOASSERTION010

tracm-test-data

Test data for the Tracm software package

010

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language:Jupyter NotebookMIT010