Beast code in Giters

Chris Ruis's repositories

MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets

Language:PythonMIT25 4 4

Summarise nucleotide counts at a set of positions in a BAM file to search for mixtures

Language:PythonGPL-3.013 4 1

Mutational spectra for SARS-CoV-2 lineages

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Materials for Bayesian phylogenetics tutorial

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Scripts to extract information from trees and tree distributions

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Repository of code and metadata used to analyse the SARS-CoV-2 sequencing data from the AGILE CST-2 phase IIa clinical trial

Language:RGPL-3.0000

Scripts used in DCC clade emergence manuscript

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Data and scripts used in "Mutational spectra analysis reveals bacterial niche and transmission routes"

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Files used in MutTui manuscript

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Files used in "Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence"

An updated pipeline for pangenome investigation

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snipit: summarise snps relative to your reference sequence

Language:PythonGPL-3.0010

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Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

Language:PythonMIT010