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Software Downloads

Software written by or contributed to by NESCent Informatics staff, sponsored scientists, and collaborators.

  • Biojavax phylo package and classes providing NEXUS and phylip file parsing and parsimony as well as UPGMA tree reconstruction for Biojava. Developed by Bohyun Lee (Google Summer of Code Student, 2007) and Richard Holland.
  • BioPrio implements various algorithms that utilise phylogenetic information to prioritise species for biodiversity conservation and provides a GUI that allows these to be utilised by conservation managers. Developed by Klaas Hartmann (Google Summer of Code Student, 2007).
  • Tajima's Q and DoFE (no source code yet). Written by Adam Eyre-Walker.
  • Dryad is a repository of data underlying scientific publications, with an initial focus on evolutionary biology and related fields. Developed by Nescent and the University of North Carolina Metadata Research Center, in coordination with a large group of Journals and Societies in evolutionary biology and ecology. (Dryad source code)
  • DQ. Calculates multi-locus (including pairwise) linkage and identity disequilibria for SNP Haplotype datasets. Look at the 'Formal Definitions' section of README.pdf to see what disequilibria DQ is capable of computing. Contributed to by Ganesh Ganapathy.
  • GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned sequence datasets using the maximum-likelihood criterion. Version 0.96 is a major revision from the previous version 0.951. It includes many new features, including the ability to perform tree inference using amino acid and codon-based models, in addition to the standard nucleotide-based models available in previous versions. On a practical level, the program is able to perform maximum-likelihood tree searches on large datasets in a number of hours. Written by Derrick Zwickl, graphical interface by Jim Balhoff.
  • GeoPhylobuilder is an ESRI ArcGIS extension that creates a spatial network, a geophylogeny, from a tree file and associated geographical data. Written by Xianhua Liu and David Kidd.
  • Maximium Size Database contains body size information for many of the largest species to occur within biological groups over the history of life, from single cells billions of years ago to the blue whale of today. The purpose of collecting data of this type is to investigate the pattern of maximum body size throughout Earth's history.
  • Natural diversity extension module to Chado and Heliconius Database. Created and written by Hilmar Lapp, Xianhua Liu, Owen McMillan, and Nassib Nassar.
  • NeXML is an exchange standard for representing phylogenetic data inspired by the commonly used NEXUS format, but more robust and easier to process. Developed by Rutger Vos, with contributions by Jason Caravas (Google Summer of Code Student, 2007) and participants of the EvoInformatics working group.
  • Phenex Curation Tool. Phenex Curation Tool is a Java-based desktop application for annotating character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format for evolutionary data. Phenex, part of Phenoscape, is hosted by the OBO project and builds on Phenote and OBO-Edit. Developed by Jim Balhoff.
  • Phenoscape Ontologies. Phenoscape is using multiple ontologies to describe variation in phenotypes across species. We have developed several new ontologies required for evolutionary biology, including the Teleost Anatomy Ontology (TAO) and the Teleost Taxonomy Ontology (TTO). As community resources, these ontologies are available within the OBO Foundry . Wasila Dahdul and Peter Midford are the maintainers of the ontologies developed by Phenoscape.
  • Phenote is a Java-based stand-alone phenotype annotation and curation tool. Contributed to by Jim Balhoff.
  • Phy* command-line topological query suite for BioSQL. Developed by James Estill (Google Summer of Code Student, 2007), being integrated into BioSQL by Hilmar Lapp.
  • The Phylobase package provides a set of S4 classes and methods for representing and manipulating phylogenetic trees and data in R, as well as the ability to import NEXUS files. Developed by Ben Bolker, Marguerite Butler, Peter Cowan, Thibaut Jombart, Steven Kembel, Brian O'Meara, and other participants of the Comparative Methods in R Hackathon.
  • The Phylodb module extends the core BioSQL schema to allow storing phylogenetic trees or reticulate networks and metadata in a simple yet extensible way. An associated Perl script loads the ITIS taxonomy into the module. Developed by Hilmar Lapp and William Piel.
  • Phylogenetic data models, parsers, and phyloinformatics "glue code". Written by participants of the NESCent Phyloinformatics Hackathon.
  • PhyloGeoViz is a web based application that generates geographic maps (using the Google Maps API) of DNA haplotype data that are often used in the course of phylogeographic analysis. Developed by Yi-Hsin Erica Tsai (Google Summer of Code Student, 2007).
  • PhyloWidget is a user-friendly and web-embeddable GUI based on Java/Processing for creating, navigating, and manipulating phylogenetic trees. Developed by Gregory Jordan (Google Summer of Code Student, 2007) and William Piel.
  • Phylr is an initial proof-of concept implementation of the PhyloWS API, making phylogenetic information available via a standard set of web services. Written by participants of the Evolutionary Database Interoperability Hackathon.
  • The RMesquite package allows one to call Mesquite module methods for comparative analyses and for file input/output. Developed by Hilmar Lapp and Wayne Maddison.
  • SNAPE (Single Node Age Prior Estimator) calculates informative prior probabilities on divergence times based on fossil occurrence data retrieved from the Paleobiology Database. Developed by Michael Nowak (Google Summer of Code Student, 2007) and Derrick Zwickl.
  • xREI is an AJAX-based web interface and visualization server for xrate and its grammar files. Developed by Lars Barquist (Google Summer of Code Student, 2007) and Ian Holmes.