GCUA 1.2 – Evaluate Codon Usage in a set of Genes

GCUA 1.2

:: 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

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

GCUA

:: MORE INFORMATION

Citation:

McInerney, J.O. (1998).
GCUA (General Codon Usage Analysis).
Bioinformatics: 14 (4) 372-373.

ScanAFLP 1-3 – Evaluate AFLP Electropherograms for Phenotyping and Marker selection

ScanAFLP 1-3

:: 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

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ScanAFLP

:: 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.

NN50-calculator 0.5 – Evaluate the Correctness of Genome Assemblies

NN50-calculator 0.5

:: DESCRIPTION

NN50-calculator (Normalized N50 calculator) is a tool for evaluating the correctness of genome assemblies.

::DEVELOPER

Veli Mäkinen, Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Python

:: DOWNLOAD

 NN50-calculator

:: 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.

Probe 2.16 – Evaluate Atomic Packing & Contact Analysis

Probe 2.16

:: 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

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Probe

:: 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. (download arrow PDF, 1.4MB)

TAP 1.8 – Calculate TAP and TAP-k to Evaluate Bioinformatics Retrieval Methods

TAP 1.8

:: DESCRIPTION

TAP calculates the TAP and TAP-k to evaluate bioinformatics retrieval methods.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Perl

:: DOWNLOAD

  TAP

:: 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

PhyRe – Evaluate Taxon Sampling in Evolutionary Studies

PhyRe

:: 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

The MoZoo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 PhyRe

:: 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.

GENERATOR 1.02b – Evaluate and Group Incoherently Annotated Genes into Subsets

GENERATOR 1.02b

:: 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

 Generator

:: 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.

QiSampler 20111215 – Evaluate Prioritization Done by Scoring Schemes and Experimental Parameters of High Throughput Biological Datasets

QiSampler 20111215

:: DESCRIPTION

QiSampler evaluates the prioritization done by experimental parameters of high throughput biological datasets.

::DEVELOPER

 QiSampler Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QiSampler

:: 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.

 

misfits 1.0 – Evaluate Goodness of Fit between Phylogenetic Model and Alignment

misfits 1.0

:: 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

  • Linux / Windows /MacOsX

:: DOWNLOAD

  misfits

:: 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.