Tag: Software

Network 10.2.0.0 – Phylogenetic Network Software

Network 10.2.0.0

:: 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

Fluxus Technology Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Network

:: MORE INFORMATION

HypoTrace – Image Analysis Software for Measuring Hypocotyl Growth and Shape

HypoTrace

:: 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.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

HypoTrace

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Matlab

:: DOWNLOAD

 HypoTrace

:: MORE INFORMATION

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.

GControl – Bayesian Genomic Control Software

GControl

:: 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

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C Compiler

:: DOWNLOAD

 GControl 

:: MORE INFORMATION

Citation:

Devlin, B. and Roeder, K (1999)
Genomic Control for Association Studies.
Biometrics 55, 997-1004.

PyRx 0.9.8 – Virtual Screening software for Computer-Aided Drug Design

PyRx 0.9.8

:: 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

  • Windows / MacOsX /  Linux

:: DOWNLOAD

PyRx

:: MORE INFORMATION

Citation

L.K. Wolf,
New software and Websites for the Chemical Enterprise,
Chemical & Engineering News 87, 31 (2009)

GAAS 1.0.0.1 – Gene Array Analyzer Software

GAAS 1.0.0.1

:: 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

GAAS

:: 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].

Oligo 7.60 – Primer Analysis Software

Oligo 7.60

:: 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.

::DEVELOPER

Molecular Biology Insights

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOSX

:: DOWNLOAD

Oligo

:: MORE INFORMATION

PhyML 2020 – Phylogeny software based on the Maximum Likelihood

PhyML 2020

:: 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.

PhyML Online Version

::DEVELOPER

Stéphane Guindon , Olivier Gascuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PhyML

:: 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.