gtonkinhill
Research group leader at Peter Mac & Doherty Institute | previously at UiO, Sanger & Cambridge | microbial genomics, statistics, machine learning
Peter MacCallum Cancer Centre & University of MelbourneAustralia
Pinned Repositories
fastbaps
A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
pairsnp
A set of scripts for calculating pairwise SNP distance
pairsnp-cpp
Fast pairwise SNP distance matrices from Multiple Sequence Alignments
pairsnp-python
panaroo
An updated pipeline for pangenome investigation
panstripe
post processing of bacterial pangenome gene presence/absence matrices
rhierbaps
rhierbaps: R implementation of hierBAPS
SC2_withinhost
TCGA_analysis
tracs
Fast pairwise transmission inference from single genome and/or metagenomic data
gtonkinhill's Repositories
gtonkinhill/panaroo
An updated pipeline for pangenome investigation
gtonkinhill/fastbaps
A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
gtonkinhill/panstripe
post processing of bacterial pangenome gene presence/absence matrices
gtonkinhill/pairsnp
A set of scripts for calculating pairwise SNP distance
gtonkinhill/TCGA_analysis
gtonkinhill/tracs
Fast pairwise transmission inference from single genome and/or metagenomic data
gtonkinhill/pairsnp-cpp
Fast pairwise SNP distance matrices from Multiple Sequence Alignments
gtonkinhill/SC2_withinhost
gtonkinhill/fasttranscluster
gtonkinhill/pneumo_withinhost_manuscript
gtonkinhill/troms-_workshop
gtonkinhill/fastq-dl
Download FASTQ files from SRA or ENA repositories.
gtonkinhill/genesearch
gtonkinhill/gtonkinhill.github.io
gtonkinhill/TransPhylo_mod
gtonkinhill/Assembly-Dereplicator
A tool for removing redundant genomes from a set of assemblies
gtonkinhill/atb-ecoli
gtonkinhill/bioconda-recipes
Conda recipes for the bioconda channel.
gtonkinhill/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.
gtonkinhill/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
gtonkinhill/labsite
gtonkinhill/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
gtonkinhill/MutTui
MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets
gtonkinhill/muttui_test_data
gtonkinhill/panstripe-manuscript
gtonkinhill/pynear
A python library for efficient KNN search within metric spaces using multiple distance functions.
gtonkinhill/relate
Software for estimating genome-wide genealogies for thousands of samples
gtonkinhill/tracm-test-data
Test data for the Tracm software package
gtonkinhill/tracs_manuscript
Supplementary code and data for the TRACS manuscript
gtonkinhill/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction