:: DESCRIPTION
Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HypoTrace takes time series of image files as input and output growth rate as well as hook angle measurements for Hypocotyls. The software comes with a build-in Graphical User Interface, which allows the software to be run under three modes: 1. Automatic mode with no user intervention, good for high quality images; 2. Semi-Auto mode with a little bit user intervention, good for fair quality images; 3. Manual mode, work for all images including really bad quality images. The three modes are designed to effectively detect the cotyledons bifurcation point under all conditions.
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Citation
Wang L., Uilecan I. V., Assadi A. H., Kozmik C. A., Spalding E. P.,
HypoTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis,
Plant Physiol. 2009, 149(4), 1632-1637.
:: DESCRIPTION
GControl is a computer program for Bayesian analysis of case-control data that controls for population stratification and cryptic relatedness. GControl performs these analyses using Markov chain Monte Carlo algorithms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Devlin, B. and Roeder, K (1999)
Genomic Control for Association Studies.
Biometrics 55, 997-1004.
:: DESCRIPTION
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process – from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design.Visit Videos page for Getting Started Screencasts. See also Starting Virtual Screening and Getting Started with PyRx tutorials.
::DEVELOPER
Molecular Graphics Laboratory , The Scripps Research Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
L.K. Wolf,
New software and Websites for the Chemical Enterprise,
Chemical & Engineering News 87, 31 (2009)
:: DESCRIPTION
GAAS (Gene Array Analyzer Software) is an integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments. It is structured in management, analysis and visualization sections that allow dealing with several gene expression dataset formats, custom differential expression data analyses, suitable visualization, and storage of results.
The software performs pre-processing of gene expression data transforming any input data structure in MS-Excel format into a built-in database-based data structure in MS-Access format, perform fast differential gene expression analyses across multiple replica experiments.
GAAS is designed for a multi-user environment, enabling each user to store its own parameter values used to perform the analyses, and define data visualization schema and format of the output data.
::DEVELOPER
Pietro Cerveri, PhD & Masseroli Marco, Ph.D
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Masseroli M, Cerveri P, Pelicci PG, Alcalay M.
GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data.
Bioinformatics 2003 April 12; 19(6): 774-775.
[Abstract], [PDF], [PubMed].
:: DESCRIPTION
Populations is a population genetic software: individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions.
:: DEVELOPER
Olivier Langella. langella@moulon.inra.fr
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
OLIGO Primer Analysis Software is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. Based on the most up-to date nearest neighbor thermodynamic data, Oligo’s search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis. OLIGO performs a range of functions for researchers in PCR and related technologies; consensus, multiplex and degenerate primers, oligonucleotide database, secondary structure, LCR and more.
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:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Primer Premier is the most comprehensive software to design and analyze PCR primers.
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology.
::DEVELOPER
Stéphane Guindon , Olivier Gascuel
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Systematic Biology, 59(3):307-21, 2010.
:: DESCRIPTION
The IOCBio project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.
::DEVELOPER
Laboratory of Systems Biology at Institute of Cybernetics.
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N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Microsc. 2011 Aug;243(2):124-40. doi: 10.1111/j.1365-2818.2011.03486.x. Epub 2011 Feb 15.
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images.
Laasmaa M, Vendelin M, Peterson P.
