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.

  

Results (159 products found)

  • Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate.  Crawford, Jeremy Chase and Drea, Christine M.. 2015, Data from: Baby on board: olfactory cues indicate pregnancy and fetal sex in a non-human primate, Dryad Digital Repository
  • Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies.  Plooij, Frans X., van de Rijt-Plooij, Hetty, Fischer, Martha and Pusey, Anne. 2015, Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies, Dryad Digital Repository
  • Data from: Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum.  Conner, Jeffrey K., Mills, Cynthia J., Koelling, Vanessa A. and Karoly, Keith. 2014, Data from: Artificial selection on anther exsertion in wild radish, Raphanus raphanistrum, Dryad Digital Repository
  • Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center.  Zehr, Sarah M., Roach, Richard G., Haring, David, Taylor, Julie, Cameron, Freda H. and Yoder, Anne D.. 2014, Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center, Dryad Digital Repository
  • Data from: Tree of sex: a database of sexual systems.  The Tree of Sex Consortium,, Ashman, Tia-Lynn, Bachtrog, Doris, Blackmon, Heath, Goldberg, Emma E., Hahn, Matthew W., Kirkpatrick, Mark, Kitano, Jun, Mank, Judith E., Mayrose, Itay, Ming, Ray, Otto, Sarah P., Peichel, Catherine L., Pennell, Matthew W., Perrin, Nicolas, Ross, Laura, Valenzuela, Nicole and Vamosi, Jana C.. 2014, Data from: Tree of sex: a database of sexual systems, Dryad Digital Repository
  • metafor: Meta-Analysis Package for R, version 1.9-3.  This product consists of an updated, new version of this software for conducting phylogenetic mixed meta-analysis models using likelihood methods. One of our working group members, Dr. Wolfgang Viechtbauer, responded to our group needs (and the needs of the broader scientific community) by adding the capability of fitting arbitrary random effects and one or more phylogenies in his meta-analysis package in R, metafor. This package was already the most powerful in R for meta-analysis with maximum likelihood model fitting, and now has significantly broader applicability to a wide range of model structures. Working group members provided significant feedback about the desired capabilities in this package, and Dr. Viechtbauer has since completed an official release of the new version of the package. New is the rma.mv function, which allows specification of an arbitrary number of random effects, and known correlation matrices. This new version was released on 5/5/2014.
  • CodonAlign: Codon alignment and analysis in Biopython.  Ruan, Z., Talevich, E., & Cock, P. 2013. CodonAlign: Codon alignment and analysis in Biopython. The CodonAlign (Bio.CodonAlign) module extends biopython to support estimations of nonsynonymous substitutions per site (dN) and synonymous substitutions per site (dS), and neutrality testing. CodonAlign currently support three counting based methods (NG86, LWL85, YN00) and maximum likelihood method to estimate dN and dS. Project specific code is available at: https://github.com/zruan/biopython/tree/master/Bio/CodonAlign.
  • Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. .  Hertweck KL (2013) Data from: Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Dryad Digital Repository. doi:10.5061/dryad.43g64
  • Data from: Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae).  Davis AM, Unmack PJ, Pusey BJ, Pearson RG, Morgan DL (2013) Data from: Ontogenetic development of intestinal length and relationships to diet in an Australasian fish family (Terapontidae). Dryad Digital Repository. doi:10.5061/dryad.h30t5
  • Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach.  Soltis DE, Mort ME, Latvis M, Mavrodiev EV, O'Meara BC, Soltis PS, Burleigh JG, de Casas RR (2013) Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach. Dryad Digital Repository. doi:10.5061/dryad.h4070 Note: This dataset is also associated with Pamela Soltis's visiting scholar project (Title: Reconstructing the Great Tree of Life)
  • Data from: Reproductive aging patterns in primates reveal that humans are distinct.  Alberts SC, Altmann J, Brockman DK, Cords M, Fedigan LM, Pusey A, Stoinski TS, Strier KB, Morris WF, Bronikowski AM (2013) Data from: Reproductive aging patterns in primates reveal that humans are distinct. Dryad Digital Repository. doi:10.5061/dryad.m327n
  • Data from: Shades of red: bird-pollinated flowers target the specific colour discrimination abilities of avian vision.  Shrestha M, Dyer AG, Boyd-Gerny S, Wong BBM, Burd M (2013) Data from: Shades of red: bird-pollinated flowers target the specific colour discrimination abilities of avian vision. Dryad Digital Repository. doi:10.5061/dryad.pj860
  • Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae).  Unmack PJ, Hammer MP, Adams M, Johnson JB, Dowling TE. 2013. Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae). Dryad Digital Repository. doi:10.5061/dryad.9v852
  • Extending PartitionFinder to automatically partition DNA and protein alignments.  Frandsen, P. Lanfear, R., & Calcott, B. 2013. Extending PartitionFinder to automatically partition DNA and protein alignments. Implements a new algorithm that uses site rates or site likelihoods to automatically partition sites in DNA and protein alignments into a best fit partitioning scheme. PartitionFinder can be downloaded from: http://www.robertlanfear.com/partitionfinder/ or github.
  • GeneValidator: Identify problems with gene predictions.  Dragan, M., Priyam, A., & Wurm, Y. 2013. GeneValidator: Identify problems with gene predictions. GeneValidator identifies problems with gene predictions and provides information based on the similarities to genes in public databases. Results of prediction validation can inform sequencing curation and improvement of approaches and tools for gene prediction. GeneValidator was designed for use by biologists who want to validate data obtained in their own laboratories.
  • Implementing Machine Learning Algorithms for Classification and Feature Selection in mothur.  Lynch, J., Iverson, K., Zaher Md. Faridee, A. 2013. Implementing machine learning algorithms for classification and feature selection in mothur. Extended mothur through implementation of the support vector machine algorithm to support a new classification and feature selection command in mothur. Project-specific code is available at https://github.com/jklynch/mothur; mothur can be downloaded from http://www.mothur.org/ and github.
  • Optimizing tree evaluation in PhyML with the BEAGLE Library. .  Fanaswala, I., Rambaut, A. Suchard, M., & Guindon, S. 2013. Optimizing tree evaluation in PhyML with the BEAGLE Library. Optimized PhyML with BEAGLE to parallelize (1) partial likelihoods computations and (2) P-matrix updating (i.e. matrix multiplication).
  • owlet.  Owlet is a query expansion preprocessor for SPARQL. It parses embedded OWL class expressions (in Manchester Syntax) and uses an OWL reasoner to replace them with FILTER statements containing the URIs of subclasses of the given class expression (or superclasses, equivalent classes, or instances).
  • Phylet: Open Tree of Life Graph Visualization and Navigation.  Phelan, C., Harp, G., & Smith, S.A. 2013. Phylet: Open Tree of Life graph visualization and navigation. Phylet is a visualization tool for phylogenetic graphs, powered by the graph database Neo4j and visualized by the JavaScript library D3. Hierarchical (rather than network) graphs are used to represent tree structures. In addition to other types of relationships, conflicts are also displayed. This application can be used by specialists and general lay audiences.
  • Phylogenetics in Biopython: Filling in the gaps.  Ye, Yanbo; Holder, Mark; Sukumaran, Jeet; Talevich, Eric. 2013. Phylogenetics in Biopython: Filling in the gaps. TreeConstruction and Consensus modules for Bio.Phylo were constructed to extend biopython support for tree construction and consensus tree algorithms. These modules add UPGMA, NJ, MP, strict consensus, majority rule, adam consensus with some branch support, and bootstrap algorithms to the current package.
  • scowl.  Scowl is a Scala library allowing a declarative approach to composing OWL expressions and axioms using the OWL API.
  • Single Node Age Prior Estimator (SNAPE).  Nowak, MD, C. Simpson, and D. Zwickl. 2007. Single Node Age Prior Estimator (SNAPE) v. 1.0. SNAPE calculates informative prior probabilities on divergence times based on fossil occurrence data retrieved from the Paleobiology Database.
  • Species Autocomplete.  Vaidya, G. 2013. Species Autocomplete. This tool provides basic Javascript and PHP code to run an autocompletion script. An included Perl script allows the ITIS-DwCA resource to be used to generate the autocompletion database (in SQLite). Further improvements may allow this software program to be integrated into websites which would like to validate the input of scientific names, either for data entry or to power searches.
  • vue2owl.  A tool for converting a VUE diagram document to an OWL ontology.
  • A server side javascript controller for phylotastic products following the MVC model.  A PoC javascript framework that invokes the right Phylotastic REST services at the right time.
  • CDAO ontology release using OBO library conventions.  The CDAO Comparative Data Analysis Ontology was revised to meet OBO library ontology standards, such as numeric class identifiers.
  • CMAPOBO.  Midford, P.E., 2012, CMAPOBO, This is a simple command line tool to generate simple OBO format (syntax version 1.2) files from ontology graphs created in the CMAP tool.
  • Data from: Testing models of sex ratio evolution in a gynodioecious plant: female frequency covaries with the cost of male fertility restoration..  Caruso CM, Case A (2012) Data from: Testing models of sex ratio evolution in a gynodioecious plant: female frequency covaries with the cost of male fertility restoration. Dryad Digital Repository. doi:10.5061/dryad.v5n09
  • DateLife.  O'Meara, B.C., L. Harmon, J. Eastman, P. Midford, T. Heath, J. Brown, M. Pennell, M. Alfaro. 2012. DateLife.org. Online database and software for returning ages of most recent common ancestors given a string of taxon names.
  • ITIS-DwCA.  The TNRS group contacted David Mitchell, ITIS Data Specialist at the NMNH, who gave us permission to make the entire ITIS database available as a DarwinCore Archive. This file was generated by dwca-hunter (https://github.com/GlobalNamesArchitecture/dwca-hunter), a Ruby program developed by the Global Names Architecture. I wrote a small script to automatically organize dwca-hunter's results, and have been running it regularly and uploading the results to http://gaurav.github.com/itis-dwca/.
  • jMatrixBrowse: Coordinate-based browsing for matrices.  Goyal, P. & Baron, C. 2012. jMatrixBrowse: Coordinate-based browsing for matrices. jQuery plugin for browsing large matrices using dragging (like Google Maps). The main features of the tool include a browsable canvas that can be panned and zoomed easily.
  • Machine learning algorithm for ecology data.  Zaher Md. Faridee, A., Iverson, K., Westcott, S. 2012. Random Forest for Mothur: A machine learning algorithm for ecology data. This implementation of the random forest algorithm enables ecologists to identify bacterial populations that are associated with differences between health and disease using mothur.
  • MASTodon: Summary and visualization of phylogenetic tree sets.  Zarins, J., Rambaut, A., Cranston, K., Redelings, B. 2012. MASTodon: Summary and visualization of phylogenetic tree sets. MASTodon looks for a common subtree in a large set of phylogenetic trees. Suitability of a subtree is measured with a MAP (maximum a-posteriori probability) score. MASTodon prunes some taxa from all trees and compares each against the MAP tree. This is the same as counting the trees that contain the subtree that is obtained if you remove the selected taxa from the trees. Command line and graphical interfaces are provided. Several pruning algorithms are available, and it is possible to add more.
  • Mesquite-o-tastic - a Mesquite package for retrieving trees from Phylotastic.  Midford, P. E. 2012. Mesquite-o-tastic - a Mesquite package for retrieving trees from Phylotastic. This is a prototype package that allows a user to retrieve a tree from phylotastic that matches the taxa present in a Mesquite character matrix. See the demo video by Arlin Stoltzfus at http://www.youtube.com/watch?v=Lak-zjwFuhQ&feature=youtube_gdata_player
  • MIAPA-ETL: NeXML to MIAPA Mapping & ISAtab Transformation.  Hauser, E., & Lapp, H. 2012. MIAPA-ETL: NeXML to MIAPA Mapping & ISAtab Transformation. MIAPA-ETL is a conversion tool to Extract, Transform, and Load (ETL) MIAPA-compliant data from NeXML files into valid ISAtab format.
  • Newick to CDAO Ingestor.  The Newick to CDAO ingestor is a Perl module. The module takes as input a tree described in Newick format and produces a CDAO representation of the tree. The module is capable of contacting the Phylotastic TNRS to resolve names and adds the result of the name resolution to the CDAO representation of the tree.
  • obo-lint.  Plugin for the Protege ontology editing environment which displays axioms which can not be represented in an OBO format serialization of the ontology.
  • Ontology and RDF model for Taxonomic Name Resolution Service results. .  Lapp H. 2012. Ontology and RDF model for Taxonomic Name Resolution Service (TNRS) results. The ontology describes the entities that make up a TNRS result and the relationship between those and those between an OTU and a TNRS resolution result. The RDF model is accompanied by an instance document and a graph visualization.
  • OpenSim grid hosting on Amazon's EC2..  Using the OpenSim software, a 6 region grid was set up on virtual machine instances at Amazon's EC2 to host the 3D environments for this project. The EC2 API tools were used to automate starting and stopping the server instances in order to reduce costs by not running the instances at night when they are not used. Monitoring software was set up to restart the OpenSim software in case of errors.
  • Optimization of TreEvo R code for Approximate Bayesian Computation.  Gates, D., Banbury, B., O'Meara, B. 2012. Optimization of TreEvo R code for approximate Bayesian computation (ABC). This project project took the original TreEvo code, found and fixed ineffeciencies within the code, and added parallelization and checkpointing.
  • Phenex 1.2.  New release of the Phenex annotation software with new features supporting collaborative editing across file sharing systems such as Dropbox.
  • Phylogeny pruner based on MapReduce with web page and services interface.  Rutger Vos, 2012. A phylotastic pruning service based on MapReduce. HIP working group of NESCent. This pruner was developed to provide automated pruning services, as part of the Phylotastic project. Given a set { S } of OTU names, and the name of a source tree, the pruner returns a topology for the OTUs that it can match from { S }. This kind of pruning can be done by recursive calls into a database (which probably would need to hit the database many times) or by loading the whole tree into memory (which might take a while to read in the file, and cost a bit of memory). The way it is done here is much cooler, because it never requires the whole tree to be in memory or in a database: the pruning is done in parallel using MapReduce. Some tests on the entire dump of the Tree of Life Web Project showed that this returns a pruned subtree within a few seconds, fast enough for a web service. The pruner has two interfaces, a web forms interface (with explanatory text and examples) and a web-services interface. The code and some documentation is available at a location indicated on the web page.
  • Phylomatic v3.  A major upgrade to this well-used tool. Phylomatic version 3 is a fork of the phylocom phylomatic code and exists only as a web service. I can now: read in trees as NeXML and CDAO, graft in taxa to the megatree, and write out in a number of formats.
  • PhyloTastic services in Galaxy.  To provide end-users with a familiar graphical user interface with which to access PhyloTastic services I have developed several wrapper classes that enable interaction with TNRS, DateLife, BabelPhysh and pruning functionality within the Galaxy web application. A demo Galaxy instance is available at http://galaxy.phylotastic.org, the source code at https://github.com/phylotastic/arch-galaxy and a screen cast that demonstrates the currently available functionality is available at http://youtu.be/kMME658xOu4
  • Phylotastic tree-pruning SADI service.  A proof-of-concept SADI-based web service which uses RDF and SPARQL to return subtrees from larger phylogenetic trees.
  • PhylotasticTreeStore.  Jim Balhoff, Karen A. Cranston, Mark T. Holder, Hilmar Lapp, Emily J. McTavish, and Enrico Pontelli. June, 2012. PhylotasticTreeStore. PhylotasticTreeStore RESTful adaptor for RDF-based tree store. It is a web2py application, which provides a RESTful interface by translating queries for trees into SPARQL queries to a triple store and then using DendroPy to translate the resulting RDF to NeXML. Built at the Phylotastic hackathon. Christopher Baron, Jeet Sukumaran, and Cam Webb provided helpful feedback.
  • Phylotastic Website.  Landing page for the Phylotastic project
  • Phylowood.js: Browser-based Interactive Animations of Ancestral Dispersal and Diversity Patterns .  Landis, M., & Bedford, T. 2012. Phylowood.js: Browser-based Interactive Animations of Ancestral Dispersal and Diversity Patterns. Phylowood enables users to visualize geographic dispersal patterns of phylogenetic units on maps overtime.
  • prototype controller as Perl CGI script .  The Perl controller coordinates stub CGI implementations of the Phylotastic TNRS, tree store, topology, and branch length services which produce correct output for one example input. However, the user may substitute real service implementations into the controller workflow via CGI parameters, allowing the services to be tested for conformance to the Phylotastic specification. Usage instructions for the CGI controller, along with example input/output files for the stub services, are provided at https://github.com/phylotastic/cgi.
  • Ranked gene tree topologies probability computation.  Ismailov, I., Degnan, J., Stadler, T. 2012. Ranked gene tree topologies probability computation. Ranked Gene Trees is a polynomial-time algorithm implementation for computing probabilities of ranked gene tree topologies given species trees.
  • Reconciliotastic.  Reconcili-o-tastic starts with a gene tree, discovers the species sources, gets a tree for the species on the fly (phylotastically), then runs reconciliation software to identify which branchings represent speciations vs duplications.
  • Taxonomy Ontology Tool (VTOTool).  Midford, P. E. 2012. Taxonomy Ontology Tool (VTOTool). This tool constructs taxonomic ontologies (e.g., Phenoscape's VTO) from multiple taxonomic sources - existing ontologies (e.g., TTO) as well as other taxonomic sources (e.g., NCBI, CoL, PBDB). As of July 2012 it generates the ontologies in an OBO format where taxonomic groups are classes and follows the conventions of the OBO rendering of the full NCBI taxonomic ontology. A earlier version of this tool was used in support of a working group.
  • Taxosaurus: A Phylotastic Taxonomic Name Resolution Service.  Taxosaurus is a meta TNRS that implements the TNRastic API. It's composed by 2 main modules (the handler_library and the processor) that sit behind an http handler. The handler_library implements the TNRastic API whereas the processor coordinates the execution of the downstream calls to the sources. The processor itself has a modular design that allows the addition of new service via adaptors that are registered through a simple JSON description.
  • TNRastic API.  The TNRastic API is a lightweight RESTful API specification that provides a generalized framework to access Taxonomic Name Resolution Services. It's composed of a set of services that are essential for name resolution.
  • Tools to convert trees of Goloboff, et al. (2009) from TNT to Newick format.  The phylogeny from Goloboff, et al. "Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups" (Cladistics 2009, 25:211-230) is a valuable resource, useful for the Phylotastic project. However, it is available only in TNT format, a nested-parenthesis format like Newick. The tree file has only numeric codes, with names encoded in a separate file. Converting this information into a single Newick tree is a 3-step process: 1. convert the TNT trees (in any of the *.tre files) to newick 2. pick the tree you want and put it in a file by itself 3. replace the numeric codes in the tree with species names from Taxon_Names_Only.tnt I developed and tested Perl scripts for steps 1 and 3. The scripts contain documentation using POD. They are available from a public repository using the URL below.
  • Towards a fully RNA-aware alignment editor with Jalview and VARNA.  Menard, A., Ponty, Y., & Procter, J. Towards a fully RNA-aware alignment editor with Jalview and VARNA. This project focused on the synchronization of Jalview and VARNA to improve jalview RNA support, with emphasis on tertiary interactions. Tertiary interactions can now be loaded from XML files (RNAML format), directly annotated from 3D experimental models (PDB files), and displayed graphically using an integrated version of the Varna software.
  • APE (Analyses of Phylogenetics and Evolution) incomplete distance extension.  Popescu, A.-A., Huber, K., & Paradis, E. 2011. APE (Analyses of Phylogenetics and Evolution) incomplete distance extension. Extends APE to handle evolutionary reconstruction from incomplete distance matrices.
  • Data from: Data archiving is a good investment..  Piwowar HA, Vision TJ, Whitlock MC (2011) Data from: Data archiving is a good investment. Dryad Digital Repository. doi:10.5061/dryad.j1fd7
  • Data from: Who shares? Who doesn't? Factors associated with openly archiving raw research data..  Piwowar HA (2011) Data from: Who shares? Who doesn't? Factors associated with openly archiving raw research data. Dryad Digital Repository. doi:10.5061/dryad.mf1sd
  • DIM SUM 2: GPU computing for an individual-based simulator of movement and demography .  Hoffman, P., Savidge, K., & Brown, J. 2011. CUDA graphics optimization for DIM SUM simulations with large scale populations and landscapes.
  • Enhancing phyloGeoRef.  Verma, A., & Iverson, K.D. 2011. PhyloGeoRef. Java library that takes a phylogenetic tree and metadata associated with taxonomic units in the tree as input; and creates a kml file that can be viewed in Google Earth. This project focused on enhancing phyloGeoRef through the addition of a GUI for non-Java users; and weighted means for node positioning.
  • Extending Jalview support for handling RNA.  Engelhardt, J., & Procter, J. 2011. Extending Jalview to handle RNA with VARNA (Visualization Applet for RNA).
  • Feeding Experiments End-user Database.  C.E. Wall, V. Gapeyev, X. Liu, and H. Lapp (2011) Feeding Experiments End-user Database. http://feedexp.org, source code at https://github.com/NESCent/feedingdb
  • lociNGS: a simple database for reformatting and displaying multi-locus datasets.  Hird, S., Brown, J., Chapman, B. 2011. lociNGS: a simple database for reformatting and displaying multi-locus datasets.
  • ontophenotype: Export ontology-based phenotype descriptions to the Encyclopedia of Life..  Ginsca, A.L., Balhoff, J. 2011. ontophenotype-eol. A Java library that generates human readable text from ontologies containing phenotype data for integration into the Encyclopedia of Life (EoL).
  • Phenoscape Knowledgebase.  Web application, database, and reasoning system integrating phenotypic data from over 50 phylogenetic publications across teleost fish with developmental genetic phenotype data from the Zebrafish Information Network (ZFIN).
  • 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
  • Protege image depictions view.  A plugin for the Protege ontology editing environment which displays images depicting instances of the selected ontology class.
  • Towards automated submission of NeXML data to TreeBASE.  Yohe, L., Vos, R., & Piel, W. 2011. Towards automated submission of NeXML data to TreeBASE. This project contributed to automation of NeXML formatted data to TreeBASE, and to related data display functionality.
  • TreeRecXML .  Packer, D. & Estill, J. 2011. TreeRecXML. Perl/BioPerl implementation of tree reconciliation representations in XML. A contribution to the Tree of Life for the Plant Sciences (iPToL) project (via https://pods.iplantcollaborative.org/wiki/display/iptol/Reconciled+Trees+in+XML).
  • total-impact.  Piwowar HA and Priem J. total-impact. http://total-impact.org, code at https://github.com/total-impact
  • API for NeXML I/O and RDF triples for BioRuby .  Priyam, A., Vos, R., & Aerts, J. 2010. BioRuby API for NeXML I/O and RDF triples. Adds support to work with RDF and NeXML in BioRuby; and provides methods to semantically annotate and query BioRuby objects.
  • 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.
  • Extending Jalview capabilities to support RNA sequence alignment, annotation, and secondary structure visualization.  Lui, L., Procter, J., and Vilella, A. 2010. Extending Jalview: Supporting Rfam RNA sequence and alignment imports and secondary structure visualizations. Extends Jalview functionality to enable RNA sequences and alignments to be imported from the Rfam database (http://rfam.sanger.ac.uk/); and supports RNA secondary structure visualizations, including relevant color schemes.
  • Galaxy phylogenetics pipeline development.  Balejko, F., & Kosakovsky Pond, S.L. 2010. Extending Galaxy: Integration of HyPhy workflows and the SLAC and PARRIS methods for inferring positive selection on coding sequences.
  • GMOD: BioPerl Enhancements.  Fields, C., Lapp, H., Stajich, J., & Jordan, G. (2010). GMOD BioPerl Enhancements. GMOD Tools for Evolutionary Biology Hackathon, BioPerl Subgroup, 8-12 November, 2010. Improved tree handling in BioPerl to enable handling very large trees or large numbers of small trees. BioPerl now supports storing such trees in a lightweight database instead of in memory. Core BioPerl 1.x code: http://bioperl.org
  • GMOD & Chado natural diversity, phenotype, and genetic modules: ND revision and proof of concept Rails implementation.  Clements, D., Dauga, D., Balhoff, J., Friesen, M., Yoder, M., Washington, N., Cain, S., Redmond, S., Vgapeyev, V., Ybendana, Y. (2010). GMOD & Chado natural diversity modules: ND revision and proof of concept Rails implementation. GMOD Tools for Evolutionary Biology Hackathon, Natural Diversity and Phenotypes in Chado Subgroup, 8-12 November, 2010. Hackathon code: https://github.com/gmodevohack
  • gmod:Galaxy integration module for interactive tools.  Pond, S.K., Balejko, F. (2010). gmod:Galaxy integration module for interactive tools. GMOD Tools for Evolutionary Biology Hackathon, Galaxy and HyPhy Subgroup, 8-12 November, 2010. Improves Galaxy's ability to integrate interactive tools, using HyPhy as the prototype application. Galaxy web home: http://galaxyproject.org/.
  • gmod:GBrowse syn2.  Hayes, R.; Buels, R.; McKay, S.. (2010). gmod:GBrowse syn2. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: JBrowse syn Subgroup, 8-12 November, 2010. GBrowse_syn refactored to fit GBrowse2 architecture; consolidated image rendering abstracted in a new class. Several new classes created under Bio::Graphics::Browser2 for object representation and rendering.
  • gmod:GMatchbox: creating a common backend for comparative genomics visualization.  Hitz, B., and Lyons, E. (2010). gmod:GMatchbox: creating a common backend for comparative genomics visualization. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: GMatchbox Subgroup, 8-12 November, 2010.
  • gmod:JBrowse extension.  Yi, H., Skinner, M., Casstevens, T., Tritt, A., & Mueller, O. (2010). gmod:JBrowse: Visualizing comparative geneomics. GMOD Tools for Evolutionary Biology Hackathon, Visualization of Comparative Genomics: JBrowse syn Subgroup, 8-12 November, 2010. Extended JBrowse through removal of the "single genome" assumption from the code and successfully displayed several genomes in parallel.
  • olishing PhyloBox: PhyloBoxWidget, Documentation, Application integration..  Hill, A., Leto, J., Pick, S. (2010). Polishing PhyloBox: PhyloBoxWidget, Documentation, Application integration. GMOD Tools for Evolutionary Biology Hackathon, PhyloBox Polishing & API Subgroup, 8-12 November, 2010.
  • 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.
  • PhyloGeoRef: A Java library for producing phylogenetic data kmls to be rendered in Google Earth..  Iverson, K.D., and Kidd, D. 2010. PhyloGeoRef: A Java library for producing phylogenetic data kmls to be rendered in Google Earth.
  • RBrownie: Ancestral State Reconstruction in R. .  Stack, J.C., O'Meara, B., Harmon, L. 2010. RBrownie: Ancestral State Reconstruction in R. Extends comparative phylogenetic analysis capabilities in R.
  • 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
  • A new flavor of PhyloWS to return TreeBASE objects in NeXML.  Piel, W., Cranston, K., Kosnik, M., & Seltmann, K. (2009). A new flavor of PhyloWS to return TreeBASE objects in NeXML. NESCent Hackathon on Evolutionary Database Interoperability, Taxonomic Intelligence Subgroup. 9-13 March, 2009, Durham, NC.
  • 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.
  • Bio.Geography: Biogeographical Phylogenetics for BioPython.  Matzke, N., & Smith, S. 2009. Bio.Geography. Bio.geography is a Biophython that enables automated searching, downloading, and parsing of geographic location records from the Global Biodiversity Information Facility (GBIF).
  • BioLib mapping for the libsequence population genetic libraries.  Shuai, X., Fields, C., Prins, P. 2009. BioLib mapping for the libsequence population genetic libraries. Extends the BioLib project by adding access to Libsequence, a C++ library for population genetic simulation and the evolutionary analysis of molecular data. Mappings to Perl and Python made available using SWIG.
  • Biopython support for parsing and writing phyloXML: Tree and TreeIO.  Talevich, E., & Chapman, B. 2009. Tree and TreeIO. Supports phyloXML use in biophython.
  • Build a Mesquite package to view Phenex-generated Nexml files.  Hayden, K., Midford, P., Balhoff, J. 2009. 'Build a Mesquite package to view Phenex-generated Nexml files', a Google summer of code project. This project resulted in a Mesquite plug-in package that used the nexml library for java to parse and display ontology-based annotations from nexml files generated by Phenex. The tool displays annotations within the Mesquite character matrix editor.
  • Dryad.  Todd Vision, Ryan Scherle, Hilmar Lapp, Jane Greenberg, Peggy Schaeffer, Kevin Clarke, Peter Midford, Mark Diggory. 2012. 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/
  • Enhanced search functionality in Phylr.  Jiao, D., & Scherle, R. 2009. Enhanced search functionality in Phylr. Enhanced Phylr service for searching content in a collection of XML files, using Lucene; and new services for searching relational databases.
  • Enhancing PhyloWidget to provide a generic, customizable web-based interface for interacting with and visualizing phylogenetic trees.  Jordan, Greg; McKay, Sheldon; Seltmann, Katja; Stoltzfus, Arlin. (2009). Enhancing PhyloWidget to provide a generic, customizable web-based interface for interacting with and visualizing phylogenetic trees. NESCent Hackathon on Evolutionary Database Interoperability, Visualization Subgroup. 9-13 March, 2009, Durham, NC. Enhancements implement methods to edit visual parameters (e.g., branch width, color, node shape); simple database searching; and tree transformations. Hackathon code: https://code.google.com/p/dbhack1/
  • Extending BEAGLE: GPU acceleration for phylogenetic inference using OpenCL.  Ayres, D., Darling, A., Suchard, M. 2009. Extending BEAGLE: GPU acceleration for phylogenetic inference using OpenCL.
  • Java API for the NeXML data model.  Midford, P., Balhoff, J., Donnelly, S., & Vos, R. (2009). Java API for the NeXML data model. NESCent Hackathon on Evolutionary Database Interoperability, Java API Library to NeXML Subgroup. 9-13 March, 2009, Durham, NC.
  • Mapping the Bio++ Phylogenetics toolkit to R/BioConductor and BioJAVA with BioLib.  Smith, A.A., & Prins, P. 2009. Mapping the Bio++ Phylogenetics toolkit to R/BioConductor and BioJAVA: A contribution to the BioLib project.
  • 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. Code at http://github.com/NESCent/max-bodysize-evol , web application at http://bodysize.nescent.org
  • PHLAWD: phylogenetic dataset construction.  Smith, S.A. (2009). PHLAWD: phylogenetic dataset construction. PHLAWD (pronounced flawd) allows for the rapid creation of large (mega) phylogenies using NCBI databases. PHLAWD takes advantage of multi threaded computers and can produce matrices of more than 100,000 taxa. Target audiences for PHLAWD include evolutionary biologists hoping to mine GenBank for data associated with their lineages, and also comparative biologists and ecologists who want to develop phylogenetic hypotheses. Binaries for MacOSX and Linux are available at: http://code.google.com/p/phlawd. It is recommended that you work with the source code for the most updated version (https://github.com/blackrim/phlawd). The manual is at the PHLAWD site: http://phlawd.net/.
  • Phylontal.  Midford, P. E. 2009. Phylontal Phylontal is a tool developed to explore phylogenetically aware alignment of multiple taxon-specific ontologies.
  • phyloXML support in BioRuby.  Jaunzeikare, D. & Zmasek, C. 2009. phyloXML support in BioRuby. 2009. Reading and writing capabilities for phyloXML in BioRuby.
  • 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.
  • Publication of GBIF Data via SADI Semantic Web Services.  Extension of the SADI (Semantic Automated Discovery and Integration) system to integrate biodiversity data. A demo SADI Web Service was created showing how GBIF (http://vocabularies.gbif.org/) data can be served via SADI (Semantic Automated Discovery and Integration). A second service was constructed that extracts taxonomy information from the UniProt protein record.
  • Semantic API for Comparative Data Analysis Ontology (CDAO).  Hyam, R., Gopalan, V., Chisham, B., Pontelli, E., Jensen, M., & Yoder, M. (2009). Semantic API for CDAO. NESCent Hackathon on Evolutionary Database Interoperability, Semantic API for CDAO Subgroup. 9-13 March, 2009, Durham, NC. Hackathon code: https://code.google.com/p/dbhack1/
  • Support for NeXML in BioPerl via Bio::Phylo.  Miller, C., Jensen, M., & Vos, R. 2009. NeXML support in BioPerl via Bio::Phylo.
  • 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.
  • Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity.  Payne JL, Boyer AG, Brown JH, Finnegan S, Kowaleski M, Krause Jr RA, Lyons SK, McClain CR, McShea DW, Novack-Gottshall PM, Smith FA, Stempien JA, Wang SC (2008) Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Dryad Digital Repository. doi:10.5061/dryad.223
  • DBGraphNav: Graphviz navigation of databases .  McMillan, P., & O'Meara, B. 2008. DBGraphNav: Graphviz navigation of databases. DBGraphNav facilitates visual graphing of relational information stored in databases. It provides a PHP framework for a website developer to display a graphical map of relational information using AT&T's Graphviz program.
  • 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.
  • Enhancing the representation of ecophylogenetic tools in R Picante.  Helmus, M., Kembel, S., Bolker, B. 2008. Enhancing the representation of ecophylogenetic tools in R Picante. Added methods to assess phylogenetic community structure; the effects of environmental variables on phylogenetic community structure; and phylogenetic structure among species interactions in the R package Picante.
  • Matrix display of phenotype annotations using ontologies in Phenote.  Wallinga, M., & Balhoff, J. 2008. Matrix display of phenotype annotations using ontologies in Phenote. Extends Phenote by adding matrix representations of annotation data. The matrix is populated by consolidating phenotype annotations into characters by finding values which descend from the same attribute within the PATO phenotype ontology; and character values are grouped by taxon and character.
  • 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.
  • Pdsimul: A Mesquite implementation of PDAP PDSIMUL.  Ackerman, M., Midford P. E., Maddison, W. P. 2008. Pdsimul: A Mesquite implementation of PDAP pdsimul, Google Summer of Code project. Project resulted in a Mesquite package (plugin) that simulated evolutionary change in multiple continuous-valued characters up a tree, effectively an extension of the DOS PDAP application of the same name.
  • 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
  • Phenoscape Website (http://phenoscape.org).  Public interface for the Phenoscape Project. Phenoscape was initiated to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions.
  • Phenote.  Jim Balhoff. 2008. Phenote - a Java-based stand-alone phenotype annotation and curation tool.
  • PhyloFinder.  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. The software home page at http://pilin.cs.iastate.edu/phylofinder/ has become unavailable, and no other location is known.
  • 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. Code at http://github.com/NESCent/plhdb , online application at http://plhdb.org
  • SAX based phyloXML support in BioPerl.  Han, M., Fields, C. 2008. SAX-based phyloXML support in BioPerl. Extends BioPerl by adding a parser to read and write phyloXML; also enabled addition of general annotations in the BioPerl Node module.
  • 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.
  • Spider comparative biology: Ontology of terms.  Ramirez, M. J., J. A. Coddington, P. Midford. 2007. Spider comparative biology: Ontology of terms.
  • Tree and data plotting in phylobase.  Cowan, P., & Bolker, B. 2008. Tree and data plotting in the phylobase project. Implements a plotting function for visualizing phylo4 and phylo4d data objects. A key feature of the functions is the use of the grid graphics interface. This interface allows more flexible plot resizing and pushing of arbitrary plots to tree tips.
  • TreeTapper: Tools to better understand biology by tapping information in phylogenies.  Brian O'Meara (2008). TreeTapper. TreeTapper is a database of methods for using phylogenies to understand evolution. Status: well-developed database schema, work is ongoing on php scripts for adding content to the database and for displaying web pages.
    Development site: http://treetapper.nescent.org
    Source code: http://code.google.com/p/treetapper/
  • TreEvo.  O'Meara, B.C. 2008. TreEvo. TreEvo (TREE + EVOlution) is an assortment of methods for understanding evolution using trees. It aims to be compatible and complementary with the wide assortment of existing packages in this area in R.
  • Vegschema 1.4.  Kleikamp, M., Spencer, N.J., Caceres, M., Peet, R.K. 2008. Vegschema 1.4. It is an international exchange standard for plot-based vegetation data that is accepted by the broader vegetation science community.
  • Biojavax.  Bohyun Lee, Richard Holland, 2007. Biojavax phylo package and classes providing NEXUS and phylip file parsing and parsimony as well as UPGMA tree reconstruction for Biojava.
  • BioPerl Population Genetics Modules.  Jason E Stajich. 2007. BioPerl Population Genetics Modules.
  • BioPrio.  Klaas Hartmann, Tobias Thierer, Rutger Vos. 2007. BioPrio. BioPrio implements various algorithms that utilize phylogenetic information to prioritize species for biodiversity conservation and provides a GUI that allows these to be utilized by conservation managers.
  • Extending Ape with a new tree parameterization (Swofford).  Bell, C., Loarie, S., Swofford, D., Waddell, P. (2007). Extending Ape with a new tree parameterization (Swofford). NESCent Hackathon on Comparative Methods in R, Divergence Time Estimation Subgroup, 10-14 December, 2007.
  • Extending Geiger with fitContinuous and fitDiscrete.  Harmon, L., Hipp, A., & Hunt. (2007). Extending Geiger with fitCountinuous and fitDiscrete. NESCent Hackathon on Comparative Methods in R, Trait Evolution Subgroup, 10-14 December, 2007. Geiger was modified to give more reliable results by a more thorough search of the likelihood surface (fitContinuous) and to deal with a more general set of discrete character models (fitDiscrete). Geiger's tree transformations improved to work for nonultrametric trees.
  • Extending the Laser package to handle diversification rate shifts using combined phylogenetic and taxonomic data.  Alfaro, M., Midford, P., Orme, D., Rabosky, D. (2007). Extending the Laser package to handle diversification rate shifts using combined phylogenetic and taxonomic data. NESCent Hackathon on Comparative Methods in R, Diversification Subgroup, 10-14 December, 2007.
  • GARLI.  Derrick Zwickl and James Balhoff. 2007. 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.
  • GeoPhylobuilder.  David Kidd and Xianhua Liu. 2007. GeoPhylobuilder is an ESRI ArcGIS extension that creates a spatial network, a geophylogeny, from a tree file and associated geographical data.
  • GMOD Wiki.  Osborne, B.I., and S. Cain. 2007. The new GMOD Wiki with complete GMOD documentation.
  • Lagrange: likelihood analysis of geographic range evolution.  Ree, R. H. and S. A. Smith. 2007. Lagrange: likelihood analysis of geographic range evolution. Lagrange is a Python package implementing likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges.
  • NeXML.  Rutger Vos, Jason Caravas and participants of the EvoInformatics working group. 2007. NeXML is an exchange standard for representing phylogenetic data inspired by the commonly used NEXUS format, but more robust and easier to process.
  • Phlyogenetics extensions in BioJava.  Lee B.Y. and R. Holland. 2007. Phlyogenetics extensions in BioJava
  • Phy*.  James Estill and Hilmar Lapp. 2007. Phy* is a command-line topological query suite for BioSQL. http://informatics.nescent.org/wiki/PhyloSoC:Command_Line_Topological_Query_Application_for_BioSQL
  • Phylobase.  Ben Bolker, Marguerite Butler, Peter Cowan, Steven Kembel, Thibaut Jombart, Aaron Mackey, Brian O'Meara, Damien de Vienne, David Orme, Derrick Zwickl, Francois Michonneau, Hilmar Lapp, Klaus Schliep. 2008. Phylobase. Defining the basic S4 classes and methods for representing and manipulating phylogenetic trees and data in R.
  • Phylogenetic & haplotype displays for GBrowse.  Okada, M.O., & Stein, L. 2007. Phylogenetic & haplotype displays for GBrowse. Extended visualization for the GBrowse Genome Browser by dividing the single large image to multiple tracks; and created a data track to display DNA alignment data for multiple target species.
  • PhyloGeoViz.  Yi-Hsin Tsai and David Kidd. 2007. 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.
  • PhyloWidget.  Gregory Jordan and William Piel. 2007. PhyloWidget is a user-friendly and web-embeddable GUI based on Java/Processing for creating, navigating, and manipulating phylogenetic trees.
  • Prototype Database of Mixed Mating System .  Susan Kalisz, Mark Johnston and members of the Mixed Mating Working Group. 2007. The prototype database integrates comprises four separate databases. 1) The mating system database contains information on estimates of selfing/outcrossing rate and/or the inbreeding coefficient measured at the population level for 475 species. 2) The inbreeding depression database contains information on estimates inbreeding depression measured across the life history (3-stage or 4-stage IBD) measured at the population level. 3) The experimental pollination database contains information at the population level on experimental tests of selfing, outcrossing, pollen limitation, reproductive assurance, timing of selfing, etc. 4) The species traits database contains data on the average morphological, phenological, life history and habitat characteristics for all 475 species in the mating system database. Significantly, all four databases contain citations to the original publications from which the data were extracted.
  • RMesquite.  H. Lapp and W. Maddison, 2010. RMesquite. The RMesquite package allows one to call Mesquite module methods for comparative analyses and for file input/output.
  • SAS code for conducting mixed-model meta-regression analysis in SAS.  Hoeksema J. D. 2007. SAS code for conducting mixed-model meta-regression analysis in SAS.
  • Summary data on local adaptation, species traits, and experimental design across 29 cross-inoculation studies of species interactions.  Hoeksema J. D. and S. Forde. 2007. Summary data on local adaptation, species traits, and experimental design across 29 cross-inoculation studies of species interactions.
  • xrateparser.  Leung, J., & Lewis, S. xrateparser. A Perl module that runs as a web application to harnesses xrate for tree generation as .png or .svg images. Trees are generated from raw .tre files (Newick format) of .stk files, and are .png or .svg images of trees to be displayed on a webpage.
  • xREI.  Lars Barquist and Ian Holmes. 2007. xREI is an AJAX-based web interface and visualization server for xrate and its grammar files.
  • PhyloDB.  Hilmar Lapp and William Piel. 2006. 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.