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poonlab's Projects

bayroot icon bayroot

Bayesian root-to-tip regression for dating reservoir sequences

bioplus icon bioplus

In-house scripts that extend the functionality of Biopython

clmp icon clmp

Genetic clustering with Markov-modulated Poisson processes

clustuner icon clustuner

Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.

colgem icon colgem

Read-only mirror of "colgem" from r-forge SVN.

comet-prot icon comet-prot

Book chapter for upcoming Springer book Computational Methods in Protein Evolution

cophylo icon cophylo

Data and scripts associated with manuscript on Tree Metrics of Cophylogeny

covizu icon covizu

Rapid analysis and visualization of coronavirus genome variation

dynsbmr icon dynsbmr

Fork of read-only mirror of the CRAN R package repository. dynsbm — Dynamic Stochastic Block Models. Homepage: http://lbbe.univ-lyon1.fr/dynsbm

fluclades icon fluclades

Genetic taxonomy of influenza A virus subtypes

gromstole icon gromstole

Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples

hexse icon hexse

Simulation of molecular evolution with overlapping reading frames

highliner icon highliner

An implementation of LANL's Highlighter web app in R for batch processing and scaling

indelrates icon indelrates

Data and scripts used for HIV-1 group M indel rate estimation project

kamphir icon kamphir

Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework

kaphi icon kaphi

Kernel-embedded ABC-SMC for phylodynamic inference

micall-lite icon micall-lite

Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping

openrdp icon openrdp

An open-source re-implementation of the RDP4 recombination detection program

ovrf-viz icon ovrf-viz

Review article on overlapping reading frames in viruses

plodex icon plodex

Interactive visualization of SARS-CoV-2 variants

poplars icon poplars

Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database

qaudiocoder icon qaudiocoder

A simple Qt-based library for encoding, decoding and converting audio files and buffers.

sierra-local icon sierra-local

Retrieve HIVdb algorithm as XML and apply locally to HIV sequences

sup icon sup

Sequencing Uncertainty Propagation

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