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Open Sustainable Technology

https://github.com/jonchang/fishtree

The R interface to the Fish Tree of Life
cran phylogeny r
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 14, 2018

  • Relevant topics? true
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  • Main Language: R
  • Commits: 212
  • Committers: 4
  • Issues: 11
  • Pull Requests: 12
  • Owner: jonchang
  • Stars: 10
  • Forks: 2
  • Packages: 1
  • Downloads: 328
https://github.com/evolbioinfo/goalign

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
alignment fasta nexus phylip phylip-alignment phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 24, 2016

  • Relevant topics? true
  • External users? true
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  • Main Language: Go
  • Commits: 619
  • Committers: 2
  • Issues: 12
  • Pull Requests: 2
https://github.com/dereneaton/ipyrad

Interactive assembly and analysis of RAD-seq data sets
assembly genomics phylogeny rad-seq
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 07, 2015

  • Relevant topics? true
  • External users? true
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  • Active? true
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  • Main Language: Jupyter Notebook
  • Commits: 3925
  • Committers: 28
  • Issues: 149
  • Pull Requests: 7
  • Owner: dereneaton
  • Stars: 70
  • Forks: 39
  • Packages: 2
https://github.com/bioconvert/bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
bam2cram bam2sam bcf2vcf bigbed2bed bioinformatics conversion convertor cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta ngs phylogeny sam2bam sequence sniffer
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 11, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 1715
  • Committers: 33
  • Issues: 47
  • Pull Requests: 62
  • Owner: bioconvert
  • Stars: 351
  • Forks: 42
  • Packages: 1
  • Downloads: 286
https://github.com/evolbioinfo/gotree

Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
gotree itol newick nexus phylogeny tree tree-structure
Added: over 1 year ago - Last Synced: about 1 year ago - Created: July 27, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Go
  • Commits: 752
  • Committers: 5
  • Issues: 17
  • Pull Requests: 4
https://github.com/tothuhien/lsd2

A phylogeny dating method using least-squares algorithms and criteria
dating least-squares phylogeny time-scaling
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 12, 2019

  • Relevant topics? true
  • External users? true
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  • Main Language: C++
  • Commits: 145
  • Committers: 41
  • Issues: 52
  • Pull Requests: 9
  • Owner: tothuhien
  • Stars: 20
  • Forks: 5
  • Packages: 0
https://github.com/pierrebarrat/treeknit.jl

TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).
arg phylogeny reassortment recombination
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 17, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Julia
  • Commits: 424
  • Committers: 5
  • Issues: 3
  • Pull Requests: 37
https://github.com/nf-core/bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
bacteria bacterial bacterial-genome-analysis genomics mapping nextflow nf-core phylogeny pipeline tree workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 09, 2019

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Nextflow
  • Commits: 225
  • Committers: 8
  • Issues: 25
  • Pull Requests: 42
  • Owner: nf-core
  • Stars: 48
  • Forks: 27
  • Packages: 0
https://github.com/chchch/sanskrit-alignment

Sequence alignment and textual reconstruction for Sanskrit texts
haskell javascript philology phylogeny sequence-alignment
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 24, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: JavaScript
  • Commits: 273
  • Committers: 4
  • Issues: 5
  • Pull Requests: 15
  • Owner: chchch
  • Stars: 9
  • Forks: 3
  • Packages: 0
https://github.com/norwegianveterinaryinstitute/alppaca

A tooL for Prokaryotic Phylogeny And Clustering Analysis
clustering nextflow phylogeny pipeline
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 14, 2020

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Nextflow
  • Commits: 525
  • Committers: 4
  • Issues: 84
  • Pull Requests: 84
https://github.com/simonpenel/light_phylogeny

Light phylogeny API for Rust
horizontal-transfer newick phylogenetic-trees phylogenetics phylogeny phyloxml reconciled-tree recphyloxml rust svg
Added: over 1 year ago - Last Synced: about 1 year ago - Created: April 15, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Rust
  • Commits: 401
  • Committers: 1
  • Issues: 1
  • Pull Requests: 0
  • Owner: simonpenel
  • Stars: 9
  • Forks: 0
  • Packages: 1
  • Downloads: 35,059
https://github.com/kharchenkolab/numbat

Haplotype-aware CNV analysis from single-cell RNA-seq
cancer-genomics cnv-detection lineage-tracing phylogeny single-cell single-cell-analysis single-cell-rna-seq spatial-transcriptomics
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 25, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 790
  • Committers: 10
  • Issues: 162
  • Pull Requests: 10
  • Owner: kharchenkolab
  • Stars: 156
  • Forks: 22
  • Packages: 1
  • Downloads: 770
https://github.com/theosanderson/taxonium

A tool for exploring very large trees in the browser
deckgl phylogenetics phylogeny react tree virus
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 24, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: JavaScript
  • Commits: 2095
  • Committers: 13
  • Issues: 96
  • Pull Requests: 157
  • Owner: theosanderson
  • Stars: 93
  • Forks: 16
  • Packages: 2
  • Downloads: 575
https://github.com/agormp/phylotreelib

Library for analyzing and manipulating phylogenetic trees
bioinformatics library phylogeny python
Added: over 1 year ago - Last Synced: about 1 year ago - Created: July 01, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 559
  • Committers: 1
  • Issues: 3
  • Pull Requests: 0
  • Owner: agormp
  • Stars: 10
  • Forks: 1
  • Packages: 1
  • Downloads: 816
https://github.com/karel-brinda/miniphy

Phylogenetic compression of extremely large genome collections [661k ↘𝟏𝟕.𝟓𝐆𝐁, BIGSIdata ↘𝟓𝟐 𝐆𝐁]
assemblies bacteria bioinformatics compression genomes indexing k-mers mof phylogenetic-compression phylogeny prophyle
Added: over 1 year ago - Last Synced: about 1 year ago - Created: July 23, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
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  • Main Language: Python
  • Commits: 293
  • Committers: 3
  • Issues: 53
  • Pull Requests: 51
https://github.com/phlorest/birchall_et_al2016

Phlorest phylogeny derived from Birchall et al. 2016 'A combined comparative and phylogenetic analysis of the Chapacuran language family'
language-family-chapacuran phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TeX
  • Commits: 39
  • Committers: 3
  • Issues: 1
  • Pull Requests: 2
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/bouckaert_et_al2012

Phlorest phylogeny derived from Bouckaert et al. 2012 'Mapping the Origins and Expansion of the Indo-European Language Family'
language-family-indo-european phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 25
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/bouckaert_et_al2018

Phlorest phylogeny derived from Bouckaert et al. 2018 'The origin and expansion of Pama–Nyungan languages across Australia'
language-family-pama-nyungan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 24
  • Committers: 3
  • Issues: 1
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/bowern_and_atkinson2012

Phlorest phylogeny derived from Bowern & Atkinson 2012 'Computational phylogenetics and the internal structure of Pama-Nyungan'
language-family-pama-nyungan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/chacon_and_list2015

Phlorest phylogeny derived from Chacon & List 2015 'Improved computational models of sound change shed light on the history of the Tukanoan languages'
language-family-tukanoan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 20
  • Committers: 3
  • Issues: 1
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/chang_et_al2015

Phlorest phylogeny derived from Chang et al. 2015 'Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis'
language-family-indo-european phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 26
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/defilippo_et_al2012

Phlorest phylogeny derived from De Filippo et al. 2012 'Bringing together linguistic and genetic evidence to test the Bantu expansion'
language-family-bantu phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/dunn_et_al2011

Phlorest phylogeny derived from Dunn et al. 2011 'Evolved structure of language shows lineage-specific trends in word-order universals'
language-family-uto-aztecan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 21
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/gray_et_al2009

Phlorest phylogeny derived from Gray et al. 2009 'Language phylogenies reveal expansion pulses and pauses in Pacific settlement'
language-family-austronesian phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 21
  • Committers: 3
  • Issues: 1
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/greenhill2015

Phlorest phylogeny derived from Greenhill 2015 'TransNewGuinea.org: An Online Database of New Guinea Languages'
language-family-huonpeninsula phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TeX
  • Commits: 20
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/grollemund_et_al2015

Phlorest phylogeny derived from Grollemund et al. 2015 'Bantu expansion shows habitat alters the route and pace of human dispersals'
language-family-bantu phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 19
  • Committers: 3
  • Issues: 2
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/honkola_et_al2013

Phlorest phylogeny derived from Honkola et al. 2013 'Cultural and climatic changes shape the evolutionary history of the Uralic languages'
language-family-uralic phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 19
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/hruschka_et_al2015

Phlorest phylogeny derived from Hruschka et al. 2015 'Detecting regular sound changes in linguistics as events of concerted evolution'
language-family-turkic phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 20
  • Committers: 3
  • Issues: 0
  • Pull Requests: 2
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/kitchen_et_al2009

Phlorest phylogeny derived from Kitchen et al. 2009 'Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East'
language-family-semitic phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 3
  • Issues: 0
  • Pull Requests: 2
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/kolipakam_et_al2018

Phlorest phylogeny derived from Kolipakam et al. 2018 'A Bayesian phylogenetic study of the Dravidian language family'
language-family-dravidian phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 24
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/lee2015

Phlorest phylogeny derived from Lee 2015 'A Sketch of Language History in the Korean Peninsula'
language-family-koreanic phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TeX
  • Commits: 19
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/lee_and_hasegawa2011

Phlorest phylogeny derived from Lee & Hasegawa 2011 'Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages'
language-family-japonic phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TeX
  • Commits: 19
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/lee_and_hasegawa2013

Phlorest phylogeny derived from Lee & Hasegawa 2013 'Evolution of the Ainu Language in Space and Time'
language-family-ainu phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 20
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/michael_et_al2015

Phlorest phylogeny derived from Michael et al. 2015 'A Bayesian Phylogenetic Classification of Tupi-Guarani'
language-family-tupi-guarani phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Turing
  • Commits: 17
  • Committers: 2
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/robinson_and_holton2012

Phlorest phylogeny derived from Robinson and Holton 2012 'Internal Classification of the Alor-Pantar Language Family Using Computational Methods Applied to the Lexicon'
language-family-alor-pantar phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 18
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/sagart_et_al2019

Phlorest phylogeny derived from Sagart et al. 2019 'Dated language phylogenies shed light on the ancestry of Sino-Tibetan'
language-family-sino-tibetan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TeX
  • Commits: 19
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/sicoli_and_holton2014

Phlorest phylogeny derived from Sicoli & Holton 2014 'Linguistic phylogenies support back-migration from Beringia to Asia'
language-family-dene-yenesian phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: OpenEdge ABL
  • Commits: 17
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/walker_and_ribeiro2011

Phlorest phylogeny derived from Walker & Ribeiro 2011 'Bayesian phylogeography of the Arawak expansion in lowland South America'
language-family-arawakan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 19
  • Committers: 3
  • Issues: 0
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/phlorest/zhang_et_al2019

Phlorest phylogeny derived from Zhang et al 2019 'Phylogenetic evidence for Sino-Tibetan origin in northern China in the Late Neolithic'
language-family-sino-tibetan phylogeny
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 13, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 20
  • Committers: 3
  • Issues: 1
  • Pull Requests: 1
  • Owner: phlorest
  • Stars: 0
  • Forks: 0
  • Packages: 0
https://github.com/keesey/phylopic

Central repository for PhyloPic
aws biology crowdsourcing illustration nextjs phylogeny phylopic sciart serverless typescript
Added: over 1 year ago - Last Synced: about 1 year ago - Created: March 27, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: TypeScript
  • Commits: 875
  • Committers: 1
  • Issues: 20
  • Pull Requests: 29
  • Owner: keesey
  • Stars: 14
  • Forks: 0
  • Packages: 0
https://github.com/tahiri-lab/phydbscan

phyDBSCAN: Building alternative phylogenetic trees using DBSCAN and Robinson and Foulds distance
bioinformatics classification clustering consensus-tree dbscan phylogeny robinson-foulds supertree
Added: over 1 year ago - Last Synced: about 1 year ago - Created: October 22, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: C++
  • Commits: 43
  • Committers: 2
  • Issues: 0
  • Pull Requests: 1