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)

  • 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.