Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

(2012) Rutger A. Vos et al.   SYSTEMATIC BIOLOGY

Understanding angiosperm diversification using small and large phylogenetic trees

(2011) S. A. Smith et al.   AMERICAN JOURNAL OF BOTANY

Telling the whole story in a 10,000-genome world

(2011) Robert G Beiko   Biology Direct

BIO::Phylo-phyloinformatic analysis using perl

(2011) Rutger A Vos et al.   BMC BIOINFORMATICS

BioRuby: bioinformatics software for the Ruby programming language

(2010) N. Goto et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

BioJava: an open-source framework for bioinformatics

(2008) R. C. G. Holland et al.   BIOINFORMATICS