:: DESCRIPTION
OD-seq is a practical and simple method to detect outliers in MSAs. It can also detect outliers in sets of unaligned sequences, but with reduced accuracy.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
OD-seq: outlier detection in multiple sequence alignments.
Jehl P, Sievers F, Higgins DG.
BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.
:: DESCRIPTION
IMgc reads recombination-rich multiple sequence alignments, and returns the largest block containing no four-gamete violations.
::DEVELOPER
Professor Murray Cox, Massey University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Jul 15;23(14):1851-3.
Recombination-filtered genomic datasets by information maximization.
Woerner AE, Cox MP, Hammer MF.
:: DESCRIPTION
JDet is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.
::DEVELOPER
[Computational Systems Biology Group @CNB-CSIC]
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Thilo Muth, Juan A. Garcia-Martin, Antonio Rausell, David Juan, Alfonso Valencia & Florencio Pazos (2012).
JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.
Bioinformatics 28(4): 584-586.
:: DESCRIPTION
RNAcode predicts protein coding regions in a a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures including synonymous/conservative mutations and conservation of the reading frame. It does not use any species specific sequence characteristics whatsoever and does not use any machine learning techniques.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011;17(4):578-94.
