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.
- 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).
- 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.
- 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.
- 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.