helayo
helayo: Reconstructing Sanskrit texts from manuscript witnesses - Published in JOSS (2022)
Phylen
Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)
https://github.com/biocore/empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
piranha
Scripts for file processing and analysis in phylogenetics and phylogeography
RBIEN
Tools for accessing the Botanical Information and Ecology Network (BIEN) database
homoplasyfinder
A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
https://github.com/chenyangkang/bird_phylogeny
Bird (avian) phylogenetic tree with bird pictures
https://github.com/agormp/treedist
Computes measures of (dis)similarity between phylogenetic trees. Provides summaries of shared and unique bipartitions.
https://github.com/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
https://github.com/banhbio/metaphylo.jl
Phylogenetic trees with metadata by Julia based on Graphs.jl and AbstractTrees.jl.