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PHYLIP (PHYLogeny Inference Package)

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include: parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Input data types include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.

Additional Information:
Tags: evolution,phylogenetics Contributor: Cost: Free
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phpMyAdmin

phpMyAdmin is an open-source tools that provides for easy management of MySQL databases through a web-based user interface. Processes that can be completed through this tool include:

database management (creation and management of users, permissions, etc.)
create and execute queries
create and view tables, database rows and fields
execute stored procedures and triggers
import and export data

Additional Information:

Requires an installation of MySQL, as well as PHP programming language and Apache web server which can be obtained at http://www.apachefriends.org/en/xampp.html

Tags: database Contributor: HH, SL Cost: Free
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Photofiltre

Photofiltre is a simple, free image editing application that offers the standard adjustment functions (Brightness, contrast, dyed, saturation, gamma correction), layers, and also artistic filters (watercolor, pastels, Indian ink, pointillism, puzzle effect). Photofiltre can also use Photoshop plug-ins.

Additional Information: Tags: graphics,image,visualization Contributor: FF, ST Cost: Free
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pgAdmin

pgAdmin is a design and management interface for the PostgreSQL database (open source object-relational database system). It is an open source administration and development platform.

The most useful features for non-programmers are:

  1. creating simple SQL queries with a syntax-highlighting SQL editor and code editor
  2. manual inserts and editing of database tables using the spreadsheet-like interface

For database administrators, pgAdmin provides a graphical interface to all the PostgreSQL features.

The program supports multiple versions of the PostgreSQL database.

Additional Information:
Tags: database Contributor: MO, CS Cost: Free
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Pegasus

Pegasus encompases a set of technologies that help workflow-based applications execute in a number of different environments including desktops, campus clusters, grids, and now clouds. Scientific workflows allow users to easily express multi-step computations, for example retrieve data from a database, reformat the data, and run an analysis. Once an application is formalized as a workflow the Pegasus Workflow Management Service can map it onto available compute resources and execute the steps in appropriate order.

Additional Information:
  • Pegasus: a Framework for Mapping Complex Scientific Workflows onto Distributed Systems. Ewa Deelman, Gurmeet Singh, Mei-Hui Su, James Blythe, Yolanda Gil, Carl Kesselman, Gaurang Mehta, Karan Vahi, G. Bruce Berriman, John Good, Anastasia Laity, Joseph C. Jacob, Daniel S. Katz. Scientific Programming Journal, Vol 13(3), 2005, Pages 219-237
  • Deelman, E., Mehta, G., Singh, G., Su, M.-H. and Vahi, K. (2006) Pegasus: mapping large-scale workflows to distributed resources. In Workflows in e-Science, edited by I. Taylor, E. Deelman, D. Gannon and M. Shields, Springer.
  • Deelman, E., Singh, G., Su, M.-H., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Berriman, G. B., Good, J., Laity, A., Jacob, J. C. and Katz, D. S. (2005). Pegasus: a framework for mapping complex scientific workflows onto distributed systems. Sci. Program. 13: 219–237. Enabling Grids for E-sciencE (EGEE). http://www.eu-egee.org/
  • Grids and Clouds: Making Workflow Applications Work in Heterogeneous Distributed Environments. Ewa Deelman. International Journal of High Performance Computing Applications OnlineFirst, published on December 4, 2009 as doi:10.1177/1094342009356432
  • Deelman, E., Gannon, D., Shields, M. and Taylor, I. (2008). Workflows and e-Science: an overview of workflow system features and capabilities. Future Generat. Comput Syst, doi:10.1016/j.future.2008.06.012.
Tags: computing,provenance,workflow Contributor: Cost: Free
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PAUP*

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. The program has a selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. It has options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.

Additional Information:

Maddison, David R., Swofford, David L. and Maddison, Wayne P. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46: 590-621

http://users.iab.uaf.edu/~derek_sikes/zool575/z575_lab20.htm

Tags: evolution,phylogenetics Contributor: RK, CS Cost: Cost-basis
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Papers

Papers is desktop electronic library and document organizer. The tool helps users organize documents in many formats, including PDF, MS Word, spreadsheets, presentations, posters, and scanned text. Papers includes dedicated space for users' articles and conference related materials, such as travel documents and posters. It includes a citation tool and a built in search engine. The search engine allows lexical and categorical searching using both free and fee-based search engines, and the subsequent importation of documents into the user's library.

Additional Information:
Tags: data storage,metadata Contributor: RL, DG Cost: Cost-basis
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Panoply Data Viewer

Panoply is a cross-platform application which plots geo-gridded arrays from netCDF, HDF and GRIB datasets. It supports the following operations:

  • Slice and plot specific latitude-longitude, latitude-vertical, longitude-vertical, or time-latitude arrays from larger multidimensional variables.
  • Combine two arrays in one plot by differencing, summing or averaging.
  • Plot lon-lat data on a global or regional map (using any of over 75 map projections) or make a zonal average lineplot.
  • Overlay continent outlines or masks on lon-lat plots.
  • Use any ACT, CPT, GGR, or PAL color table for scale colorbar.
  • Save plots to disk GIF, JPEG, PNG or TIFF bitmap images or as PDF or PostScript graphics files.
  • Export lon-lat map plots in KMZ format.
  • Export animations as AVI or MOV video or as a collection of invididual frame images.
  • Explore remote THREDDS and OpenDAP catalogs and open datasets served there.

To be plotted by Panoply, dataset variables must be tagged with metadata information using a convention such as CF.

Additional Information:
Tags: analyze,geospatial,graphics,map,visualization Contributor: FF, GW Cost: Free
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oXygen

Oxygen is a XML editor that provides XML document validation and includes a SVN client for collaboration and a text editor, the Oxygen Author. It supports all XML technologies, including editors for XSLT, XPath, XQuery, and XML schema and DTDs. It provides intelligent XML editing with autocomplete features and content sensitive XML assistance. Management support for relational databases and native XML databases is provided. Oxygen can be used as a standalone application, or as a plugin for Eclipse or Java Webstart application. This is a commercial application, however it is offered for free to non-profit entities working in certain domains, including Ecology, through their 'Support Life' program.

Additional Information: Tags: XML Contributor: Cost: Cost-basis
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Outwit

The Outwit suite of Firefox extensions that allows you to harvest materials on the web. The suite currently includes Outwit Hub, Outwit Images, and Outwit Docs.

OutWit Hub allows you to automatically browse through pages, collect and format data and information on the web. It will automatically explore series of Web pages or search engine results for you and extract contacts, links, images, data, news, etc. You can use the Hub's default scraping utilities to help you extract data with explicit structures in the HTML source code of the page, such as lists or tables. Also, you can build scripts that will navigate from page to page in sequences of results and automatically extract quantities of information objects. Results can be exported into MS Excel.

OutWit Images is a Firefox extension for simple image browsing. With OutWit Images, as you explore the web for pictures, you can create, save, and share collections. Also, you can automatically explore Web pages or search engine results for pictures, and create, save and share your collections. OutWit Images can create full-screen slideshows for image collections.

Additional Information:

* There is a "full" version of Outwit Hub (Pro) available for a charge. Click here for comparison of the free and licensed versions:
http://www.outwit.com/products/hub/

Tags: data mining,discover,image,web services Contributor: SL, RD Cost: Free
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