:: DESCRIPTION
LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Auton and McVean,
Recombination rate estimation in the presence of hotspots.
Genome Research 17(8):1219-27, 2007.
:: DESCRIPTION
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. In particular it is designed to display summarized and annotated trees produced by BEAST.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
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:: DESCRIPTION
PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.
::DEVELOPER
Owen Marshall at Murdoch Childrens Research Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Owen J. Marshall
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Bioinformatics (2004) 20 (15): 2471-2472.
:: DESCRIPTION
ProteinModelerABC is an evolutionary framework to estimate the best-fitting substitution model of protein evolution, among a set of complex substitution models that cannot be analyzed with traditional phylogenetic likelihood functions, with the approximate Bayesian computation (ABC) approach.
::DEVELOPER
David Ferreiro, Catarina Branco, Miguel Arenas
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ferreiro D, Branco C, Arenas M. 2024.
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.
Bioinformatics, 40:3, btae096. https://doi.org/10.1093/
:: DESCRIPTION
ProtASR is an evolutionary framework to reconstruct ancestral protein sequences accounting for structural constraints.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Arenas M, Bastolla U.
ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability.
Methods Ecol Evol. 2020; 11: 248–257. https://doi.org/10.1111/2041-
:: DESCRIPTION
POPGENE is a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. This package provides the Windows graphical user interface that makes population genetics analysis more accessible for the casual computer user and more convenient for the experienced computer user. Simple menus and dialog box selections enable you to perform complex analyses and produce scientifically sound statistics, thereby assisting you to adequately analyze population genetic structure using the target markers.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
GeneFinder is a software package for linkage analysis with a variety of extensions. GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ZincExplorer is a web server that could predict Zinc-binding sites from protein sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Mol Biosyst. 2013 Sep;9(9):2213-22. doi: 10.1039/c3mb70100j.
ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.
Chen Z, Wang Y, Zhai YF, Song J, Zhang Z.
:: DESCRIPTION
piNet is a resource for interactively exploring modular network models of plant immune response.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Dong X., Jiang Z., Peng Y-L., Zhang Z. (2015)
Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis.
Plant Physiol. 2015 Mar;167(3):1186-203. doi: 10.1104/pp.114.254292.
:: DESCRIPTION
WDRR is a new WD40 Repeat Recognition method, which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments.
::DEVELOPER
Ziding Zhang’s Lab, China Agricultural University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Theor Biol. 2016 Jun 7;398:122-9. doi: 10.1016/j.jtbi.2016.03.025.
Identification of WD40 repeats by secondary structure-aided profile-profile alignment.
Wang C, Dong X, Han L, Su XD, Zhang Z, Li J, Song J