phylogenetic-trees

There are 12 repositories under phylogenetic-trees topic.

pyCirclize
moshi4 / pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
bioinformatics circos matplotlib python chord-diagram comparative-genomics genomics genomics-visualization microbial-genomics visualization phylogenetic-trees data-visualization dataviz radar-chart
Language:Python 960
YuLab-SMU / ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
annotations ggplot2 phylogenetic-trees r visualization
Language:R 883
ponnhide / pyCircos
python Circos
biopython circos circos-plot matplotlib phylogenetic-trees python visualization
Language:Python 353
veg / phylotree.js
Interactive viewer of phylogenetic trees
d3js phylogenetic-trees vizualisation
Language:JavaScript 173
biobakery / phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools biobakery phylogenetic-trees
Language:Python 138
cogent3 / cogent3
Comparative Genomics Toolkit 3
bioinformatics pycogent statistics data-science biology genomics evolution biopython markov-chain molecular-evolution non-stationary phylogenetic-trees phylogenetics python parallel signal-processing maximum-likelihood biological-sequence-analysis sequence-alignment
Language:Python 132
YuLab-SMU / treeio
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
exporter parser phylogenetic-trees
Language:R 102
biobakery / graphlan
High-quality circular representations of taxonomic and phylogenetic trees
biobakery circular-visualization phylogenetic-trees python taxonomic-trees tools
Language:Python 95
MicrobeTrace
CDCgov / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-visualization hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:TypeScript 94
shawnlaffan / biodiverse
A tool for the spatial analysis of diversity
spatial-analysis phylogeography phylogenetic-trees phylogenetic-diversity phylodiversity endemism beta-diversity species-turnover randomisations biodiverse hacktoberfest
Language:Perl 77
caravagnalab / revolver
Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
transfer-learning cancer-evolution cancer-genomics phylogenetic-trees clustering
Language:R 65
lczech / genesis
A library for working with phylogenetic and population genetic data.
c-plus-plus phylogenetics evolutionary-placement phylogenetic-data phylogenetic-trees phylogenetic-placements placement population-genetics pool-sequencing
Language:C++ 61
LKremer / CAFE_fig
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
cafe gene-families evolution molecular-evolution ete3 phylogenetic-trees
Language:Python 61
vinuesa / get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
phylogenomics population-genetics phylogenomics-pipeline species-trees markers genomics pipeline phylogenetics phylogenetic-trees codon-alignment maximum-likelihood orthologues species-delimitation microbiology core-genome perl r bash clock-hypothesis recombination
Language:Perl 59
vibbits / phyd3
Phylogenetic tree viewer based on D3.js
d3js phylogenetic-trees visualization
Language:JavaScript 56
phyTreeViz
moshi4 / phyTreeViz
Simple phylogenetic tree visualization python package for phylogenetic analysis
phylogenetic-trees bioinformatics biopython matplotlib python visualization
Language:Python 48
r_phylogenetics_worshop
agmcfarland / r_phylogenetics_worshop
Using ggtree to build phylogenetic trees
phylogenetic-trees visualization workshop
Language:HTML 46
cmzmasek / archaeopteryx-js
Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.
archaeopteryx visualization javascript phylogenetics evolution phylogenetic-trees analysis archaeopteryx-js
Language:JavaScript 40
albertyw / itolapi
Python API for the Interactive Tree of Life (iTOL)
python visualization phylogenetic-trees phylogenetics bioinformatics computational-biology
Language:Python 38
cmzmasek / forester
forester is a collection of open source libraries of Java and Ruby software for phylogenomics and evolutionary biology research
biology computational-biology evolution genomics java phylogenetic-trees phylogenetics ruby visualization
Language:Java 36
daijiang / rtrees
rtrees: an R package to assemble phylogenetic trees from mega-trees
r rstats r-package phylogenetic-trees
Language:R 33
TreeDist
ms609 / TreeDist
Calculate distances between phylogenetic trees in R
r r-package rstats phylogenetic-trees tree-distances trees
Language:R 33
JTFouquier / ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
python python3 phylogenetics phylogenetic-trees diversity fungi fungal microbiome microbiology microbial-ecology bioinformatics
Language:Python 30
LKremer / showTree
showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
gene-families protein-families ete3 python protein-domains phylogenetic-trees phylogenetics visualization treeview
Language:Python 30
mooreryan / iroki
Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.
bioinformatics phylogenetic-trees ecology microbial-ecology visualization
Language:HTML 30
moshi4 / CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
bioinformatics molecular-evolution evolution phylogenetic-trees phylogenetics python matplotlib phylogenomics
Language:Python 29
ncbi / tree-tool
Incremental building of phylogenetic distance trees
data-analysis phylogenetic-trees bioinformatics distance-measures evolution bioinformatics-tool
Language:HTML 28
davidemms / SHOOT
SHOOT.bio - the phylogenetic search engine
phylogenetic-trees
Language:Python 24
TreeTools
ms609 / TreeTools
Create, modify and analyse phylogenetic trees in R
phylogenetics phylogenetic-trees evolutionary-biology r-package cran
Language:R 23
jangevaare / PhyloTrees.jl
Phylogenetic trees in Julia
bioinformatics julia phylogenetic-trees phylogenetics
Language:Julia 21
PlantDr430 / BuscoOrthoPhylo
Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs
alignment busco comparative-genomics orthofinder phylogenetic-trees
Language:Python 20
thirdkind
simonpenel / thirdkind
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
phylogeny phylogenetic-trees reconciliation recphyloxml phylogenetics rust
Language:Rust 19
ramithuh / diff-evol-tree-search
We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.
combinatorial-optimization computational-biology phylogenetic-trees
Language:Python 18
Quartet
ms609 / Quartet
R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
phylogenetics bioinformatics research-tool quartet tree cran phylogenetic-trees quartet-distance comparison
Language:C++ 15
AABoyles / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics epidemiology network-graph hiv cdc pathogens phylogenetics phylogenetic-trees phylogeny phylogenomics network-visualization network-analysis genomics genomics-visualization genomic-data-analysis sequence-alignment
Language:HTML 13
Picani / fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
phylogeny phylogenetic-trees bioinformatics-tool command-line-tool rust sqlite sqlite3 ncbi-taxonomy-database ncbi newick
Language:Rust 13