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phyloXML: XML for evolutionary biology and comparative genomics

Mira V Han and Christian M Zmasek*

BMC Bioinformatics 2009, 10:356  doi:10.1186/1471-2105-10-356

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BioMed Central: 6 citations

Research article   Open Access Highly Accessed

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

Anna Sheydina, Ruth Y Eberhardt, Daniel J Rigden, Yuanyuan Chang, Zhanwen Li, Christian C Zmasek, Herbert L Axelrod, Adam Godzik BMC Bioinformatics 2014, 15:112 (17 April 2014)

Software   Open Access Highly Accessed

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes

Michiel Van Bel, Sebastian Proost, Christophe Van Neste, Dieter Deforce, Yves Van de Peer, Klaas Vandepoele Genome Biology 2013, 14:R134 (13 December 2013)

An online tool for processing assembled RNA-seq data and performing functional, comparative and phylogenetic analyses

Software   Open Access Highly Accessed

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan BMC Bioinformatics 2013, 14:158 (13 May 2013)

Data Note   Open Access Highly Accessed

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, Sudhir Kumar, Dan F Rosauer, Rutger A Vos BMC Research Notes 2012, 5:574 (22 October 2012)

This article is part of a collection on Data standardization...

As part of our series on data sharing Arlin Stoltzfus and colleagues call for a standardized system for handling information from phylogenetic trees, including centralized data deposition, and user friendly means of data retrieval and integration.

Software   Open Access Highly Accessed

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

Eric Talevich, Brandon M Invergo, Peter JA Cock, Brad A Chapman BMC Bioinformatics 2012, 13:209 (21 August 2012)

Software   Open Access Highly Accessed

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

Ben C Stöver, Kai F Müller BMC Bioinformatics 2010, 11:7 (5 January 2010)