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Top 9 phylogeny open source projects

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

✭ 15

c C++perl reconciliation ensembl neighbor-joining maximum-likelihood phylogeny species-trees gene-trees

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.

✭ 26

perl pipeline genomics ngs variants epidemiology phylogeny tuberculosis

phyr

Functions for phylogenetic analyses

✭ 23

r C++bayesian glmm inla phylogeny rpackage species-distribution-modeling

ipyrad

Interactive assembly and analysis of RAD-seq data sets

✭ 57

Jupyter Notebook python genomics phylogeny rad-seq

l1ou

Detection of evolutionary shifts in Ornstein-Uhlenbeck models

✭ 15

r C++c phylogeny ornstein-uhlenbeck study-trait-evolution evolutionary-shift

machina

Framework for Metastatic And Clonal History INtegrative Analysis

✭ 28

Jupyter Notebook C++TeX shell python CMake r sequencing migration phylogeny metastasis comigration polyclonal reseeding monoclonal

bactmap

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

✭ 36

Nextflow groovy python HTML workflow tree pipeline genomics mapping bacteria phylogeny bacterial nf-core bacterial-genome-analysis

taxonium

A tool for exploring very large trees in the browser

✭ 65

javascript python HTML react tree virus phylogenetics phylogeny deckgl

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

✭ 37

javascript python HTML CSS visualization bioinformatics microbiome ordination phylogeny qiime biplot qiime2 tree-plot

1-9 of 9 phylogeny projects