:: DESCRIPTION
RecPars performs a parsimony analysis of a set of DNA sequences. It tries to find the best phylogenies for different segments of the sequences and thereby postulating a recombination event between these segments.
::DEVELOPER
Bioinformatics Research Centre (BiRC),Aarhus University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MotifOrganizer is designed to cluster large sets of DNA sequence motifs to identify common patterns. Different motif widths are allowed. It uses a two-stage divide-conquer-combine strategy to achieve scalability and efficiency.
::DEVELOPER
Steve Qin @ the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MOTIFREGRESSOR for discovering sequence motifs upstream of genes that undergo expression changes in a given condition. The method combines the advantages of matrix-based motif finding and oligomer motif-expression regression analysis, resulting in high sensitivity and specificity. MOTIF REGRESSOR is particularly effective in discovering expression-mediating motifs of medium to long width with multiple degenerate positions.
::DEVELOPER
Xiaole Shirley Liu Lab , Erin Marie Conlon
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Conlon, E.M., Liu, X.S., Lieb, J.D., Liu, J.S. (2003)
Integrating regulatory motif discovery and genome-wide expression analysis.
Proceedings of the National Academy of Sciences USA, 100, 3339-3344.
:: DESCRIPTION
Vector NTI Viewer, a freeware program, allows scientists to study and analyze biological molecules. It incorporates a small subset of functions from the much more sophisticated Vector NTI Suite software.Vector NTI Viewer can read Vector NTI Molecule Documents, and molecule data from GenBank, EMBL or FASTA files. You may also paste molecule descriptions in one of the above formats from the Clipboard. In addition, the Viewer can read plain nucleotide sequence data form ASCII file or the Clipboard, automatically creating a virtual annotated molecule for that nucleotide sequence.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The Vector NTI Viewer is free.
:: DESCRIPTION
Ameliorator is a freeware program that calculates forward and backwards amelioration times for DNA sequence evolution.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DNA Master is a freeware DNA sequence editor and analysis package.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
DNA Counter is a freeware tool that shows the proportions of A,C G, T nucleotides and CG, AT nucleotides in a DNA sequence.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects. It is particularly suited to working with chromatogram files from ABI machines, and is one of the few programs able to edit as well as view these files. The program has powerful DNA translation and restriction enzyme analysis facilities, and works with external programs to produce multiple alignments and contigs with ease.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
If you find the program useful, don’t forget to register – you will receive the latest version which already has a number of significant improvements over the evaluation version.
:: DESCRIPTION
VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome-scale. The software, i) allows estimating a number of population genetic parameters; ii) conducts the analysis by using the sliding window or a wavelet transform-based methods to capture relevant information from DNA polymorphism data; iii) permits the visualization of the results by commonly used genome browsers.
::DEVELOPER
Molecular Evolutionary Genetics Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hutter, S., Vilella, A, J. and Rozas, J. (2006).
Genome-wide DNA polymorphism analyses using VariScan.
BMC Bioinformatics 7: 409.
