phylogenetic-trees

There are 11 repositories under phylogenetic-trees topic.

YuLab-SMU / ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
annotations ggplot2 phylogenetic-trees r visualization
Language:R 834
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 717
ponnhide / pyCircos
python Circos
biopython circos circos-plot matplotlib phylogenetic-trees python visualization
Language:Python 334
veg / phylotree.js
Interactive viewer of phylogenetic trees
d3js phylogenetic-trees vizualisation
Language:JavaScript 169
biobakery / phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
python tools biobakery phylogenetic-trees
Language:Python 121
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 101
YuLab-SMU / treeio
:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
exporter parser phylogenetic-trees
Language:R 94
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 88
biobakery / graphlan
High-quality circular representations of taxonomic and phylogenetic trees
circular-visualization taxonomic-trees phylogenetic-trees python tools biobakery
Language:Python 85
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 75
caravagnalab / revolver
REVOLVER - Repeated Evolution in Cancer
cancer-evolution cancer-genomics clustering phylogenetic-trees transfer-learning
Language:R 64
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 59
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++ 56
vibbits / phyd3
Phylogenetic tree viewer based on D3.js
d3js phylogenetic-trees visualization
Language:JavaScript 56
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 51
r_phylogenetics_worshop
agmcfarland / r_phylogenetics_worshop
Using ggtree to build phylogenetic trees
phylogenetic-trees visualization workshop
Language:HTML 45
phyTreeViz
moshi4 / phyTreeViz
Simple phylogenetic tree visualization python package for phylogenetic analysis
bioinformatics biopython matplotlib phylogenetic-trees python visualization
Language:Python 38
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 36
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 35
albertyw / itolapi
Python API for the Interactive Tree of Life (iTOL)
python visualization phylogenetic-trees phylogenetics bioinformatics computational-biology
Language:Python 33
daijiang / rtrees
rtrees: an R package to assemble phylogenetic trees from mega-trees
phylogenetic-trees r r-package rstats
Language:R 31
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 ecology microbial-ecology phylogenetic-trees visualization
Language:HTML 29
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 28
TreeDist
ms609 / TreeDist
Calculate distances between phylogenetic trees in R
r r-package rstats phylogenetic-trees tree-distances trees
Language:R 28
moshi4 / CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result
bioinformatics molecular-evolution evolution phylogenetic-trees phylogenetics python matplotlib phylogenomics
Language:Python 25
davidemms / SHOOT
SHOOT.bio - the phylogenetic search engine
phylogenetic-trees
Language:Python 24
jangevaare / PhyloTrees.jl
Phylogenetic trees in Julia
bioinformatics julia phylogenetic-trees phylogenetics
Language:Julia 22
PlantDr430 / BuscoOrthoPhylo
Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs
alignment busco comparative-genomics orthofinder phylogenetic-trees
Language:Python 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 17
TreeTools
ms609 / TreeTools
Create, modify and analyse phylogenetic trees in R
phylogenetics phylogenetic-trees evolutionary-biology r-package cran
Language:R 16
ncbi / tree-tool
Incremental building of phylogenetic distance trees
bioinformatics bioinformatics-tool data-analysis distance-measures evolution phylogenetic-trees
Language:C++ 14
thirdkind
simonpenel / thirdkind
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
phylogeny phylogenetic-trees reconciliation recphyloxml phylogenetics rust
Language:Rust 14
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
AABoyles / MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
bioinformatics cdc epidemiology genomic-data-analysis genomics genomics-visualization hiv network-analysis network-graph network-visualization pathogens phylogenetic-trees phylogenetics phylogenomics phylogeny sequence-alignment
Language:HTML 11
DomBennett / treeman
:deciduous_tree::man: An R package for manipulating phylogentic trees
bioinformatics cran evolution phylogenetic-trees
Language:R 11