:: DESCRIPTION
NN50-calculator (Normalized N50 calculator) is a tool for evaluating the correctness of genome assemblies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Oct 3;13:255. doi: 10.1186/1471-2105-13-255.
Normalized N50 assembly metric using gap-restricted co-linear chaining.
Mäkinen V, Salmela L, Ylinen J.
:: DESCRIPTION
ScanAFLP : a R script to evaluate AFLP electropherograms for phenotyping and marker selection based on peak height distribution and repeatability using blind controls.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Herrmann D., Poncet B. N., Manel S., Rioux D., Gielly L., Taberlet P., Gugerli F (2010)
Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.
Molecular Ecology 53:302-310.
:: DESCRIPTION
Merqury is a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.
::DEVELOPER
Maryland Bioinformatics Labs (MarBL)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rhie A, Walenz BP, Koren S, Phillippy AM.
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Genome Biol. 2020 Sep 14;21(1):245. doi: 10.1186/s13059-020-02134-9. PMID: 32928274; PMCID: PMC7488777.
:: DESCRIPTION
GCUA (General Codon Usage Analysis) is designed to perform various tasks that are of use for evaluating codon usage in a set of genes. You can get it to do some simple things like calculate the number of observations of a particular codon in a gene. Or you can do the same thing for the combined dataset. You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole). The program also produces a distance matrix based on the similarity of codon usage in genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
McInerney, J.O. (1998).
GCUA (General Codon Usage Analysis).
Bioinformatics: 14 (4) 372-373.
:: DESCRIPTION
QiSampler evaluates the prioritization done by experimental parameters of high throughput biological datasets.
::DEVELOPER
Computational Biology and Data Mining (CBDM) Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Res Notes. 2011 Mar 9;4:57.
QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards.
Fontaine JF, Suter B, Andrade-Navarro MA.
:: DESCRIPTION
Probe allows one to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
For a detailed description see Word, et al. (1999), “Visualizing and Quantifying Molecular Goodness-of-Fit: Small-probe Contact Dots with Explicit Hydrogen Atoms” J. Mol. Biol. 285, 1709-1731. (
:: DESCRIPTION
TAP calculates the TAP and TAP-k to evaluate bioinformatics retrieval methods.
::DEVELOPER
Statistical Computational Biology Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
H.D. Carroll, M.G. Kann, S.L. Sheetlin, and J.L. Spouge
“Threshold Average Precision (TAP-k): a Measure of Retrieval Efficacy Designed for Bioinformatics”
(2010) Bioinformatics 26 : 1708-1713
:: DESCRIPTION
PhyRe (Phylogenetic Representativeness) is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics, it makes possible to evaluate taxon coverage within a given ingroup.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLAZZI F., FERRUCCI R.R., PASSAMONTI M. (2010)
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies.
BMC BIOINFORMATICS, 11:209.
:: DESCRIPTION
Generator (GENElist Research Aimed Theme-discovery executOR) is a tool to evaluate and group incoherently annotated genes into subsets according to their gene ontology (GO) terms.
::DEVELOPER
Petri Pehkonen ( Petri.Pehkonen@uku.fi)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Pehkonen P, Wong G and Toronen P. (2005)
Theme discovery from gene lists for identification and viewing of multiple functional groups.
BMC Bioinformatics. 2005; 6: 162.
:: DESCRIPTION
misfits is a computer program to evaluate the goodness of fit between a phylogenetic model and an alignment.It offers a look back at the alignment to pinpoint to site patterns that do not fit to the model and the resulting tree (thereafter referred to as the tree-model). MISFITS then introduces a number of extra-substitutions on the tree, in a parsimonious manner to fit these site patterns in to the tree-model. These extra-substitutions plus the evolutionary model will then fully explain the alignment. Thus, the number of extra-substitutions may be interpreted as a measure to evaluate the goodness of fit of the model to the alignment: the less the number, the better the fit.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Minh Anh Thi Nguyen, Steffen Klaere, and Arndt von Haeseler (2010)
MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment.
Mol. Biol. Evol., 28:143-152.
