:: DESCRIPTION
The TreePack program uses a tree-decomposition based algorithm to solve the side-chain packing problem more efficiently. This algorithm is more efficient than SCWRL 3.0 while maintaining the same level of accuracy.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Jinbo Xu and Bonnie Berger.
Fast and accurate algorithms for protein side-chain packing.
The Journal of the ACM, Volume 53, Issue 4 (July 2006), pp. 533-557.
:: DESCRIPTION
GeoAssign is a Web based program assigns test individuals according to their genotypes or metric traits to groups (e.g. country of origin, population of origin) which are defined by reference individuals. Thus, the user needs to upload one data file for the test individuals (“Test file”) and one data file for the reference individuals (“Reference file”). The assignment is done using a nearest neighbour approach.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Degen B, Blanc-Jolivet C, Stierand K, Gillet E.
A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin.
Forensic Sci Int Genet. 2017 Mar;27:132-141. doi: 10.1016/j.fsigen.2016.12.011. Epub 2016 Dec 29. PMID: 28073087.
:: DESCRIPTION
MIMA is a method for the alignment of GC/MS data and MCC/IMS data facilitating the identification of biomarker molecules.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Maurer F, Hauschild AC, Eisinger K, Baumbach J, Mayor A, Baumbach JI (2014).
MIMA – A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements.
Int. J. Ion Mobil. Spec. Volume 17, Issue 2, pp 95-101.
:: DESCRIPTION
EMPANADA is a tool for evidence-based, non-uniform, and sample-specific assignment of gene families to pathways in metagenomic data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MBA ,Model-Based Assignment, is a Java program for automated assignment and assessment of uncertainty of protein backbone NMR. It is based on a statistical model for NMR spectra, and employs a tree-based algorithm of stochastic optimization.
::DEVELOPER
Laboratory for Statistical Proteomics and Bioinformatics , Purdue University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
O. Vitek, J. Vitek, B. A. Craig, C. Bailey-Kellogg.
“Model-based assignment and inference of protein backbone nuclear magnetic resonances”
Statistical Applications in Genetics and Molecular Biology, 3: Article 6, 2004.
:: DESCRIPTION
mude (multivariate decoy database analysis) is a set of programs implementing the framework to assess MS/MS spectra assignments
:: DEVELOPER
By Cerqueira, Fabio (fabio.cerqueira@ufv.br); Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.
Cerqueira FR, Graber A, Schwikowski B, Baumgartner C.
J Proteome Res. 2010 May 7;9(5):2265-77. doi: 10.1021/pr901023v.