phylogeny

There are 4 repositories under phylogeny topic.

• bioconvert / bioconvert

  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

  ngsbam2samconversionphylogenysequencesam2bambam2crambcf2vcfbigbed2bedcram2bamcram2samembl2enaembl2fastaembl2genbankfasta2fastqgenbank2emblgenbank2fastasnifferbioinformaticsconvertor
  Language:Python 351

• eaton-lab / toytree

  A minimalist tree plotting library using toyplot graphs

  phylogenyplottingpythontree
  Language:Jupyter Notebook 159

• kharchenkolab / numbat

  Haplotype-aware CNV analysis from single-cell RNA-seq

  cancer-genomicscnv-detectionsingle-cellphylogenysingle-cell-analysissingle-cell-rna-seqspatial-transcriptomicslineage-tracing
  Language:R 148

• evolbioinfo / gotree

  Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

  gotreeitolnewicknexusphylogenytreetree-structure
  Language:Go 108

• YuLab-SMU / treedata-book

  :books: a complete reference book for treeio, tidytree and ggtree packages

  tidytreetreeioggtreevisualizationdata-importdata-manipulationphylogeny
  Language:TeX 99

• theosanderson / taxonium

  A tool for exploring very large trees in the browser

  phylogeneticsphylogenytreedeckglreactvirus
  Language:JavaScript 89
• MicrobeTrace

  CDCgov / MicrobeTrace

  The Visualization Multitool for Molecular Epidemiology and Bioinformatics

  bioinformaticsepidemiologynetwork-visualizationhivcdcpathogensphylogeneticsphylogenetic-treesphylogenyphylogenomicsgenomicsgenomics-visualizationgenomic-data-analysissequence-alignment
  Language:TypeScript 83

• dereneaton / ipyrad

  Interactive assembly and analysis of RAD-seq data sets

  rad-seqphylogenyassemblygenomics
  Language:Jupyter Notebook 68

• evolbioinfo / goalign

  Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

  alignmentfastanexusphylipphylip-alignmentphylogeny
  Language:Go 62

• nf-core / bactmap

  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

  nf-corenextflowworkflowpipelinebacteriabacterialbacterial-genome-analysisphylogenymappinggenomicstree
  Language:Nextflow 47

• biocore / empress

  A fast and scalable phylogenetic tree viewer for microbiome data analysis

  bioinformaticsbiplotmicrobiomeordinationphylogenyqiimeqiime2tree-plotvisualization
  Language:JavaScript 45

• bmaitner / RBIEN

  Tools for accessing the Botanical Information and Ecology Network (BIEN) database

  rbiodiversityecologybotanicalplantopen-sciencephylogenytraitsrange-mapsbien
  Language:HTML 40

• ropensci / rotl

  Interface to Open Tree of Life API

  rrstatsr-packagetaxonomyphylogenypeer-reviewed
  Language:R 39

• ngs-fzb / MTBseq_source

  MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

  tuberculosispipelinephylogenyvariantsepidemiologyngsgenomicsmycobacterium-tuberculosis
  Language:Perl 38
• EToKi

  zheminzhou / EToKi

  all methods related to Enterobase

  phyloassemblyphylogenyspadesmlstgenotype
  Language:Python 36

• raphael-group / machina

  Framework for Metastatic And Clonal History INtegrative Analysis

  phylogenymigrationmetastasissequencingcomigrationpolyclonalreseedingmonoclonal
  Language:Jupyter Notebook 33

• prophyle / prophyle

  Accurate, resource-frugal and deterministic DNA sequence classifier.

  metagenomicsbwtphylogenymetagenomic-classificationbioinformaticsbacteriavirusesburrows-wheeler-transformk-mersphylogenetic-compressionsimplitigsprophyle
  Language:Python 31

• daijiang / phyr

  Functions for phylogenetic analyses

  bayesianglmminlaphylogenyrrpackagespecies-distribution-modeling
  Language:R 28

• Ensembl / treebest

  TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)

  phylogenymaximum-likelihoodneighbor-joiningreconciliationensemblgene-treesspecies-trees
  Language:C 20

• karel-brinda / Phylign

  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

  assembliesbacteriabioinformaticscompressiongenomesindexingk-mersmofphylogenetic-compressionphylogeny
  Language:Python 20

• tothuhien / lsd2

  A phylogeny dating method using least-squares algorithms and criteria

  datingphylogenyleast-squarestime-scaling
  Language:C++ 20

• JosephCrispell / homoplasyFinder

  A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

  phylogenyindelsnucleotide-alignmentconsistencymutationshomoplasy
  Language:R 18

• khabbazian / l1ou

  Detection of evolutionary shifts in Ornstein-Uhlenbeck models

  phylogenyornstein-uhlenbeckstudy-trait-evolutionevolutionary-shift
  Language:R 18

• ropensci / brranching

  I can haz all the phylogenies

  rstatsphylogenyphylogeniesrr-package
  Language:R 18

• bediger4000 / malware-phylogeny

  malware phylogeny for WSO web shell, Shellbot IRC bot and algorithm

  irc-botmalwaremalware-phylogenyphylogenyshellbotweb-shell
  Language:Perl 16
• PlantPhylomoji

  ghuertaramos / PlantPhylomoji

  Dataset and scripts to create a Phylogeny of Plant Emojis

  emojiggtreephylogeneticsphylogenyplants
  Language:Jupyter Notebook 14

• keesey / phylopic

  Central repository for PhyloPic

  phylogenysciarttypescriptawsbiologycrowdsourcingillustrationnextjsserverlessphylopic
  Language:TypeScript 13

• Picani / fastax

  Make phylogenetic trees and lineages from the NCBI Taxonomy database

  phylogenyphylogenetic-treesbioinformatics-toolcommand-line-toolrustsqlitesqlite3ncbi-taxonomy-databasencbinewick
  Language:Rust 13

• banhbio / Taxonomy.jl

  Julia package to handle the NCBI Taxonomy database.

  bioinformaticsjuliaphylogenybiodiversityncbincbi-databasencbi-taxonomytaxonomy
  Language:Julia 12

• lmc297 / bactaxR

  Bacterial taxonomy construction and evaluation in R

  taxonomyphylogenyaverage-nucleotide-identityanimedoid-genomesbacteriabacterial-species
  Language:R 12

• Colelyman / kleuren

  Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees

  bioinformaticsde-bruijn-graphsphylogeneticsphylogeny
  Language:C++ 11

• jananiravi / compbio-gists

  Computational Biology & Bioinformatics Resources

  computational-biologybioinformaticsrshellmolecular-evolutionphylogenycomparative-genomicstranscriptomicsdata-sciencegists
  Language:Shell 11

• justincbagley / piranha

  Scripts for file processing and analysis in phylogenetics and phylogeography

  bayesian-inferencemaximum-likelihoodphylogenyphylogeographypopulation-structurershellsnpssshsupercomputer
  Language:Shell 11

• agormp / phylotreelib

  Library for analyzing and manipulating phylogenetic trees

  bioinformaticslibraryphylogenypython
  Language:Python 10

• karel-brinda / MiniPhy

  Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴 𝗚𝗶𝗕 | AllTheBact'23 ↘𝟵𝟯𝗚𝗶𝗕]

  assembliesbacteriabioinformaticscompressiongenomesindexingk-mersmofphylogenetic-compressionphylogenyprophyle
  Language:Python 10

• NorwegianVeterinaryInstitute / ALPPACA

  A tooL for Prokaryotic Phylogeny And Clustering Analysis

  phylogenyclusteringnextflowpipeline
  Language:Nextflow 10