bayroot
Bayesian root-to-tip regression for dating reservoir sequences
2021
ArtPoon, RouxCil
gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
2021
ArtPoon, DBecker7, GopiGugan, ebrintn
Candescence
2021
V Bettauer, M Hallett
tuning-disorder-virus
Ensemble classifier of intrinsic protein disorder for viruses
2020
ArtPoon, galmog, Abayomi-Olabode
covizu
Rapid analysis and visualization of coronavirus genome variation
2020
ArtPoon, GopiGugan, bonnielu, RouxCil, MomomomoLiu, horaciobam, kwade4, SandeepThokala, nav-mohan, babarlelephant, Abayomi-Olabode, dpannguyen, ewong347, SyouTono242, ebrintn
sam2conseq
None
2020
ArtPoon
clustuneR
Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.
2019
ConnorChato, ArtPoon
sup
Sequencing Uncertainty Propagation
2019
DBecker7, davidchampredon, ArtPoon, ConnorChato, GopiGugan
ovrf-viz
Review article on overlapping reading frames in viruses
2019
horaciobam, ArtPoon
ggfree
ggplot2-style plots with base R graphics
2019
ArtPoon
OpenRDP
An open-source re-implementation of the RDP4 recombination detection program
2019
kwade4, ArtPoon, GopiGugan, SandeepThokala, brj1, dpannguyen
Poplars
Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database
2019
kwade4, ArtPoon
highlineR
An implementation of LANL's Highlighter web app in R for batch processing and scaling
2018
Lisa-Monique, ArtPoon
tn
Optimization of genetic clustering methods by predictive modeling
2018
ConnorChato, ArtPoon
HexSE
Simulation of molecular evolution with overlapping reading frames
2018
horaciobam, kwade4, ArtPoon, GopiGugan, SandeepThokala
MIxT: fast prototyping software
2018
V Dumeaux, B Fjukstad, M Hallett
MIxT: breast tumor and blood transcriptional profiles
2018
V Dumeaux, B Fjukstad, M Hallett
Website and courses
2018
M Hallett
STROMA4
2018
S Saleh, M Hallett
MIxT: web service
2018
B Fjukstad, Lars Ailo Bongo, V Dumeaux, M Hallett
twt
Generic framework for the coalescent simulation of pathogen trees within host trees in R
2017
gtng92, ArtPoon, helenhe96, RouxCil, davidchampredon, GopiGugan, R3IDV3, 0ldM4j0r
BioID
Source files for online resources of Bioinformatics of Infectious Diseases course
2017
ArtPoon
vindels
Developing an empirical model of sequence insertion and deletion in virus genomes
2017
jpalmer37, ArtPoon
sierra-local
Retrieve HIVdb algorithm as XML and apply locally to HIV sequences
2017
ArtPoon, jzpero, gtng92, GopiGugan, MathiasRenaud, WilliamZekaiWang, SandeepThokala
Kaphi
Kernel-embedded ABC-SMC for phylodynamic inference
2016
gtng92, ArtPoon, MathiasRenaud, 0ldM4j0r, helenhe96, brj1
clmp
Genetic clustering with Markov-modulated Poisson processes
2016
ArtPoon, rmcclosk, gtng92, 0ldM4j0r
MiCall-Lite
Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping
2016
donkirkby, ArtPoon', emartin-cfe', rng64', dfornika'
gotoh2
Lightweight and customizable Python/C extension for pairwise alignment of genetic sequences using the Gotoh algorithm
2016
ArtPoon, RouxCil
git-raw
2015
A Tofigh
BreSect
2014
A Tofigh, M Suderman, M Hallett
AIMS
2014
E Paquet, M Hallett
AIPS
2017
E Paquet, M Hallett
pslt
2004
M Scott, M Hallett