COCOA 2.8.0 – Coordinate Covariation Analysis

COCOA 2.8.0

:: DESCRIPTION

COCOA is a method for understanding epigenetic variation among samples. COCOA can be used with epigenetic data that includes genomic coordinates and an epigenetic signal, such as DNA methylation and chromatin accessibility data.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R
BioConductor

:: DOWNLOAD

COCOA

:: MORE INFORMATION

Citation

Lawson JT, Smith JP, Bekiranov S, Garrett-Bakelman FE, Sheffield NC.
COCOA: coordinate covariation analysis of epigenetic heterogeneity.
Genome Biol. 2020 Sep 7;21(1):240. doi: 10.1186/s13059-020-02139-4. PMID: 32894181; PMCID: PMC7487606.

ERC – Evolutionary Rate Covariation Analysis

ERC

:: DESCRIPTION

ERC measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories.

::DEVELOPER

Department of Computational and Systems Biology , University of Pittsburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

ERC analysis: web-based inference of gene function via evolutionary rate covariation.
Wolfe NW, Clark NL.
Bioinformatics. 2015 Aug 4. pii: btv454.

CovaRNA / CovStat 1.16.0 – Detecting Long-range Covariations in Nucleotide Alignments

CovaRNA / CovStat 1.16.0

:: DESCRIPTION

CovaRNA / CovStat is a novel index-based computational method to detect long-range covariation on a genomic scale, as well as for determining the statistical significance of observed covariation patterns in alignment pairs.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C / R

:: DOWNLOAD

CovaRNA / CovStat

:: MORE INFORMATION

Citation:

Bindewald E, Shapiro BA.
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.
RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25. PMID: 23887147; PMCID: PMC3753924.

doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences

doublet 1.0

:: DESCRIPTION

doublet is a modified version of the Smith-Waterman algorithm that incorporates patterns of dipeptide covariation to align protein sequences.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

doublet

:: MORE INFORMATION

Citation:

Gavin A. Price, Gavin E. Crooks, Richard E. Green and Steven E. Brenner
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
Bioinformatics 21 (20): 3824-3831.