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antigenic-thrift-with-oas

Antigenic thrift model for a three-locus biallelic system which includes the effect of Original Antigenic Sin on population dynamics

beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees

bottleneck_size_estimation

Estimate the bottleneck using MLHapRec & SAMFIRE

covid-19

Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE

dtpcourse2018

haplotype_reconstruction

Uses SAMFIER variant calling package to reconstruct haplotypes

iran-covid19

Data and codes for processing COVID19 (the novel Corona virus) data in Iran

iran_study

iran_weeklymortality

oxford-poster

LaTeX beamer poster template themed for the University of Oxford

planets

popgen-notes

Population genetics notes

pow_model

PoW model calculates the time to the most recent common ancestor of virus species

ppin

protein-protein interaction networks: finding their fractal dimension

samfire

Multi-locus variant calling from short-read sequence data

saphire

Modelling transmission dynamics of COVID-19, while accounting for presymptomatic infectiousness, time-varying ascertainment rates, transmission rates and population movements.

siv_hiv_evolution

sobemovirus_genus

treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

treetime_examples

A collection of documented examples using TreeTime

tui.image-editor

🍞🎨 Full-featured photo image editor using canvas. It is really easy, and it comes with great filters.

twoclock_rate

vaccine_preventable_deaths