phylogeny
There are 198 repositories under phylogeny topic.
bioconvert/bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
kharchenkolab/numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
eaton-lab/toytree
A minimalist tree plotting library using toyplot graphs
evolbioinfo/gotree
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
theosanderson/taxonium
A tool for exploring large trees in the browser
YuLab-SMU/treedata-book
:books: a complete reference book for treeio, tidytree and ggtree packages
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
evolbioinfo/goalign
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
dereneaton/ipyrad
Interactive assembly and analysis of RAD-seq data sets
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
biocore/empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
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.
ropensci/rotl
Interface to Open Tree of Life API
bmaitner/RBIEN
Tools for accessing the Botanical Information and Ecology Network (BIEN) database
zheminzhou/EToKi
all methods related to Enterobase
karel-brinda/MiniPhy
Phylogenetic compression of extremely large genome collections [661k βππ²ππΆπ | BIGSIdata βπ°π΄ππΆπ | AllTheBact'23 βπ³π±ππΆπ]
karel-brinda/Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
daijiang/phyr
Functions for phylogenetic analyses
prophyle/prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
raphael-group/machina
Framework for Metastatic And Clonal History INtegrative Analysis
tothuhien/lsd2
A phylogeny dating method using least-squares algorithms and criteria
keesey/phylopic
Central repository for PhyloPic
Ensembl/treebest
TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)
JosephCrispell/homoplasyFinder
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
khabbazian/l1ou
Detection of evolutionary shifts in Ornstein-Uhlenbeck models
ropensci/brranching
I can haz all the phylogenies
simonpenel/thirdkind
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
bediger4000/malware-phylogeny
malware phylogeny for WSO web shell, Shellbot IRC bot and algorithm
ghuertaramos/PlantPhylomoji
Dataset and scripts to create a Phylogeny of Plant Emojis
agormp/phylotreelib
Library for analyzing and manipulating phylogenetic trees
JRaviLab/compbio-gists
Computational Biology & Bioinformatics Resources
banhbio/Taxonomy.jl
Julia package to handle the NCBI Taxonomy database.
PierreBarrat/TreeKnit.jl
TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).
lmc297/bactaxR
Bacterial taxonomy construction and evaluation in R
NorwegianVeterinaryInstitute/ALPPACA
A tooL for Prokaryotic Phylogeny And Clustering Analysis
zhangrengang/subgenome_phasing_example
An Example of Subgenome Phasing for Complex Allopolyploidy