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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.
  • 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 heuristic maximum likelihood phylogenetic searches on large biological sequence datasets. 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.
  • 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.
  • 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.
  • 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.