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Software and Databases

Software and databases contributed by NESCent Informatics staff, sponsored scientists, and collaborators. If you have products as results from NESCent-sponsored projects, please report your products through our online web application.

  

Recent Products (25 products found)

• phytools: Phylogenetic Tools for comparative biology (and other things).  Revell, L. J. 2011. phytools: Phylogenetic Tools for comparative biology (and other things). R package version 0.0-8. http://CRAN.R-project.org/package=phytools
• BAli-Phy version 2.1.0.  (Released 7/7/2010) BAli-Phy is a Bayesian MCMC program for estimating phylogenies and sequence alignments jointly from unaligned sequence data. BAli-Phy can estimate phylogenies without bias toward a guide tree, when the alignment is uncertain.
  
  New features in the 2.1.0 release include:
  • Allow multiple separate genes as input
  • Each gene may have a different substitution or indel model
  • Decrease the amount of RAM used.
  • Speed up the analysis for many taxa (e.g. > 30).
  • Auto-detect step sizes in slice sampling.
• Phenoscape Ontologies.  Wasila Dahdul and Peter Midford. 2010. 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.
• TreeBASE.  TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. A second-generation version of TreeBASE was released in 2010 and is hosted by NESCent.
  Source code: http://sf.net/projects/treebase
• beagle-lib: A general purpose library for evaluating the likelihood of sequence evolution on trees.  Alexei Drummond. 2009. A project to create an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This will allow these packages to make use of implementations that make use of optimized hardware such as graphics processing units.
• Dryad.  Todd Vision, Ryan Scherle, Hilmar Lapp, Jane Greenberg, Peggy Schaeffer, Kevin Clarke. 2009. Dryad - 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.
  Source code: http://dryad.googlecode.com/
• MATICCE.  Andrew L. Hipp and Marcial Escudero. 2009. MATICCE - a software package in the R language that employs an information-theoretic approach to infer shifts in continuous character distribution on phylogenetic trees. MATICCE also provides simulation functions for visualizing analysis results, functions for accounting for phylogenetic and model uncertainty, and helper functions for the ouch R package.
• Maximum Size Database.  Jonathan Payne, Jennifer Stempien, Hilmar Lapp, Xianhua Liu, Michal Kowalewski. 2009. Maximum Size Database. 2009. Phanerozoic Body Size Trends through Time and Space Working Group. National Evolutionary Synthesis Center.
• Phylr.  Participants of the Evolutionary Database Interoperability Hackathon. 2009. Phylr is an initial proof-of concept implementation of the PhyloWS API, making phylogenetic information available via a standard set of web services.
• VertNet: global museum database of vertebrate natural history collections.  Constable, H and Russell, L. 2009. VertNet is a global museum database of vertebrate natural history collections. Four distributed database networks (MaNIS, HerpNET, ORNIS and FishNet) have been the result of a massive, collaborative effort within the museum and bioinformatics communities to make specimen data interoperable, mappable and publicly available. VertNet was formed as an umbrella project to meet the common needs of the participants, maintain the existing networks, add new members and develop integrated online technologies.
• A collection of data sets for phylogenetic analysis.  Qiu, WG. 2007. A collection of data sets for phylogenetic analysis.
• BioPerl module for reading nexml file.  Qiu, WG. 2008. A new BioPerl module for reading nexml file. Bio::TreeIO:nexml
• Brownie.  O'Meara, B.C. 2008. Brownie 2.1. Brownie is a program for analyzing rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. It now also implements many other methods for examining trait evolution and methods for doing species delimitation. See below for info on downloading the program. http://www.brianomeara.info/brownie
• Comparative Data Analysis Ontology (CDAO).  Prosdocimi, F., B. Chisham, E. Pontelli, J.D. Thompson, and A. Stoltzfus. 2008. Comparative Data Analysis Ontology (CDAO), an OWL-DL ontology for evolutionary comparative analysis.
• DQ.  Ganeshkumar Ganapathy, Nihshanka Debroy. DQ: A python package for multilocus disequilibria.
• Dupertree.  Wehe, A., M.S. Bansal, J.G. Burleigh, and O. Eulenstein. 2008. Dupertree: a program for large-scale gene tree parsimony phylogenetic analyses. Dupertree describes a new program for inferring phylogenies by gene tree parsimony. It is also publicly available. Other software used to build supertrees and identify ancient large-scale duplication events in the above manuscripts will eventually be released to the public.
• MIAPA annotation tool.  Stoltzfus, A. 2008. MIAPA annotation tool (proof-of-concept software). To demonstrate the potential for users to construct their own ontology-based MIAPA annotations, as in the knowledge capture experiment below, we have created a proof-of-concept application by adapting Phenote. The result is an interactive graphical tool for user-generated, ontology-bound MIAPA annotations.
• MrFisher.  O'Meara, B.C. 2008. MrFisher. This program a slight modification of MrBayes to do simulated annealing maximum likelihood tree searches (Bayes is credited with inventing Bayesian statistics, Fisher with inventing likelihood).
• Nexus Class Library.  Lewis, Holder, et al. 2008. Nexus Class Library. The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.
• Phenex.  Jim Balhoff. 2008. Phenex - an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data
• Phenote.  Jim Balhoff. 2008. Phenote - a Java-based stand-alone phenotype annotation and curation tool.
• PhyloFinder.  Gordon Burleigh, Chen, D., J.G. Burleigh, M.S. Bansal, and D. Fernandez-Baca. 2008. PhyloFinder: an intelligent search engine for phylogenetic tree databases. BMC Evol. Biology 8:90.] describes a new software tool for accessing data from tree databases. A prototype is publicly available.
• PhyloWS.  Lapp, H., Vos R. (2008) PhyloWS: A standard web service-interface for phylogenetic data and service providers.
• Primate Life Histories Database.  Hilmar Lapp, Xianhua Liu, members of the Primate Life Histories Working Group. Primate Life Histories Database. This database contains individual-based life history data that have been collected from wild primate populations by nine working group participants over a minimum of 19 years. The purpose of collecting data of this type is to make comparative analyses that can shed light on the population dynamics and the social and ecological adaptations that have shaped both human and nonhuman primate evolution.
  Source code: http://sf.net/projects/plhdb
• Simple Image LinKing (SILK).  Maddison, W. P., and M. J. Ramirez. 2006. Simple Image LinKing (SILK): A Mesquite package for associating images with character matrices.