DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.
Keywords for this software
References in zbMATH (referenced in 8 articles )
Showing results 1 to 8 of 8.
- Pouryahya, Fatemeh; Sankoff, David: Peripheral structures in unlabelled trees and the accumulation of subgenomes in the evolution of polyploids (2022)
- Jaffe, Ariel; Amsel, Noah; Aizenbud, Yariv; Nadler, Boaz; Chang, Joseph T.; Kluger, Yuval: Spectral neighbor joining for reconstruction of latent tree models (2021)
- N. Moshiri: TreeSwift: A massively scalable Python tree package (2020) not zbMATH
- Alexander J. Gates; Yong-Yeol Ahn: CluSim: a python package for calculating clustering similarity (2019) not zbMATH
- Russell Y. Neches; Camille Scott: SuchTree: Fast, thread-safe computations with phylogenetic trees (2018) not zbMATH
- Christensen, Sarah; Molloy, Erin K.; Vachaspati, Pranjal; Warnow, Tandy: Optimal completion of incomplete gene trees in polynomial time using OCTAL (2017)
- Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
- Berk Ekmekci, Charles E. McAnany, Cameron Mura: An Introduction to Programming for Bioscientists: A Python-based Primer (2016) arXiv