phylogenetic-analysis

There are 3 repositories under phylogenetic-analysis topic.

edgardomortiz / vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
vcf snps phylip alignment phylogenetics nexus binary snapp fasta outgroup convert-snps vcf-files phylogenetic-analysis vcf-format phylip-matrix haploid diploid polyploid
Language:Python 263
KlausVigo / phangorn
Phylogenetic analysis in R
phylogenetic-analysis phylogenetics r
Language:R 197
LinguaPhylo / linguaPhylo
LinguaPhylo: A language for describing, visualising and simulating probabilistic phylogenetic models
probabilistic-models beast2 phylogenetic-analysis revbayes reproducibility
Language:Java 14
btmartin721 / raxml_ascbias
Script for removing or counting invariant sites for the RAxML ascertainment bias corrections
raxml phylogenetics phylogenetic-data phylogenetic-analysis ascertainment-bias correction dna-sequences dna-sequence-analysis filtering sequence-alignment variant-sites invariant-sites lewis felsenstein stamatkis
Language:Python 13
phyloviz / phyloviz-web-platform
A Modular and Web-Based Tool for Phylogenetic Analysis
data-processing phylogenetic-analysis data-centric-workflows data-visualization
Language:TypeScript 7
cparsania / phyloR
An R package to prepare data for phylogenetic analysis
phylogenetic-analysis ncbi-blast taxonomy rpackage phylogenetics
Language:R 4
hansiu / MatPhylobi
a tool for automatic construction of molecular data matrix for phylogenetic inference based on GenBank records
phylogenetics phylogenetic-analysis phylogenetic-data supermatrix-phylogenetic-analyses supermatrix genbank tool molecular-markers
Language:Python 4
AKU-CITRIC-Center-for-Bioinformatics / ncov
Genomic Epidemiology of SARS-CoV-2 in Pakistan
github nextflow yaml genomics epidemiology genomics-visualization epidemiology-analysis epidemiology-models pyhylodynamics phylogenetics phylosurveillance phylogenomics phylogenetic-analysis phylogenetic-data phylogenetic-trees phylogeography phylogenomics-pipeline
3
phyloviz / phyloviz-main
Phylogenetic Inference and Data Visualization for Sequence-Based Typing Methods
data-visualization phylogenetic-analysis phylogenetic-inference sequence-based-typing-methods
Language:Java 3
phyloviz / phyloDB
A Framework for Large Scale Phylogenetic Analysis
data-processing data-storage graph-database phylogenetic-analysis
Language:Java 2
Bader-Research / GRAPPA
GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
phylogenetics phylogenetic-trees biology phylogenetic-analysis
Language:C 1
Fly-annotation
DhakadPankaj / Fly-annotation
A comparative annotation toolkit (CAT) pipeline for 304 fly genomes.
annotation-tool busco cactus genome-alignment genome-annotation molecular-evolution phylogenetic-analysis comparative-annotation-toolkit
Language:Shell 1
mbrazeau / morphy.archive
Morphy releases are archived here. This project serves as the root folder for all of the source projects in Morphy.
phylogenetics phylogenetic-analysis morphology discrete-character-data
Language:Python 1
wiegertj / EBG
Tool for estimating the Felsenstein bootstrap support of phylogenetic trees
boosting-ensemble phylogenetic-analysis phylogenetics
Language:Python 1
Alexis-Marion / Sequential-trait-evolution-sharks
Github repository for "Sequential trait evolution did not drive deep-time diversification in sharks" article, published in Evolution
extinction speciation-rates diversification phylogenetic-analysis trait-evolution
Language:Jupyter Notebook 0
duartebred / Algoritmos-Analise-Sequencias-Biologicas
Repositório para apresentação de código desenvolvido pelo grupo 3 para a UC Algoritmos para Análise Sequências Biológicas do Mestrado em Bioinformática, ano lectivo 23-24.
alignment-algorithm blast dynamic-programming motifs needleman-wunsch-algorithm orfs phylogenetic-analysis recursion-algorithm string-manipulation translation
Language:Jupyter Notebook 0
iliapopov17 / BI-Phylogenetics
Repository for accumulating the complete pipeline of phylogenetic studies
phylogenetics study-project phylogenetic-analysis phylogenetic-trees phylogeny
Language:Jupyter Notebook 0
clabe-wekesa / SATO
A python pipeline that brings together tools for generation of consensus sequence, multiple sequence alignment, and phylogenetic analysis.
consensus-sequence fasttree mrbayes multiple-sequence-alignment phylogenetic-analysis sequence-cleaner
Language:Python
erathorn / StatLing
This is the StatLing Repository.
mcmc phylogenetic-analysis linguistics
Language:Python
fhdsl / GDSCN_SARS_RStudio_on_AnVIL
Lab module and lectures for identifying phylogenetic history of SARS variants using R
anvil gdscn phylogenetic-analysis sars-cov-2
Language:CSS
propan2one / OshV-1-molepidemio
Code of the article that describes the molecular epidemiology analyses of OsHV-1 virus by whole genome sequencing approaches in French shellfish growing areas.
bioinformatics bioinformatics-pipeline metagenomics virology r molecular-epidemiology ngs-analysis shell-scripts academic-project academic-paper genome virus-genomes genomes-comparison phylogenetic-analysis analysis
Language:Shell
SimonGreenhill / COEDLSS
COEDL Summer School 2019 - Language Phylogenies Tutorial
phylogenetic-analysis beast language-phylogeny