ReproPhylo: An Environment for Reproducible Phylogenomics

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

(2014) Todd H Oakley et al.   BMC BIOINFORMATICS

Mating system shifts and transposable element evolution in the plant genus Capsella

(2014) J Ågren et al.   BMC GENOMICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

The Dawn of Open Access to Phylogenetic Data

(2014) Andrew F. Magee et al.   PLoS One

Phylogenomics provides strong evidence for relationships of butterflies and moths

(2014) A. Y. Kawahara et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Journals unite for reproducibility

(2014) M. McNutt   SCIENCE

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

The Availability of Research Data Declines Rapidly with Article Age

(2013) Timothy H. Vines et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

phyloGenerator: an automated phylogeny generation tool for ecologists

(2013) William D. Pearse et al.   Methods in Ecology and Evolution

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis

(2011) Brandon Chisham et al.   BMC BIOINFORMATICS

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

(2011) R. Sanchez et al.   NUCLEIC ACIDS RESEARCH

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

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

Methodology capture: discriminating between the "best" and the rest of community practice

(2008) James M Eales et al.   BMC BIOINFORMATICS

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH