:: DESCRIPTION
SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gouy M., Guindon S. & Gascuel O. (2010)
SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
Molecular Biology and Evolution 27(2):221-224.
:: DESCRIPTION
VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Before you download software you need to read disclaimer.
:: DESCRIPTION
AlignExIn ( Align Exon Intron) is a handy and useful utility built in order to display the alignment of exons. The program displays the exon painted in red and the alignments painted in blue by default, but it is possible to change the colors.All you have to do is select the input files (fasta and exon) and the program will do the rest.
::DEVELOPER
Institute of Bioinformatics WWU Muenster
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.
SLPFA is an improved subcellular location predictor of SLP-Local
::DEVELOPER
Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2007 Nov 30;8:466.
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
Tamura T, Akutsu T.
:: DESCRIPTION
The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Arenas M.
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation.
Bioinformatics. 2021 Aug 27:btab617. doi: 10.1093/bioinformatics/btab617. Epub ahead of print. PMID: 34450622.
:: DESCRIPTION
ASpipe (alternative splicing) is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments.ASpipe extracts coordinates and scores for high-quality intron/exon/alignments from the original program outputs and stores them in MySQL5.0 databases.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang, B.-B., O’Toole, M., Brendel, V. & Young, N.D. (2008)
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.
BMC Plant Biol. 8:17.
:: DESCRIPTION
SAPS (statistical analysis of protein sequences) calculates all the statistics for any individual protein sequence input.
SSPA is an acronym for Significant Segment Pair Alignment.
::DEVELOPER
The Brendel Group @ Indiana University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SAPS
Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992)
Methods and algorithms for statistical analysis of protein sequences.
Proc. Natl. Acad. Sci. USA 89, 2002-2006.
SSPA
Karlin, S., Weinstock, G. & Brendel, V. (1995)
Bacterial classifications derived from RecA protein sequence comparisons.
J. Bacteriol. 177, 6881-6893.
:: DESCRIPTION
MPAlign-editor is a graphical tool for DNA and Protein sequences and alignments.
::DEVELOPER
Frederico Arnoldi (fgcarnoldi@gmail.com)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MPAlign editor: uma ferramenta gráfica e intuitiva para alinhamentos moleculares.
Frederico GC Arnoldi 2005
Proceedings of II Workshop TIDIA—FAPESP
:: DESCRIPTION
NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.
:: DESCRIPTION
GCAligner is a software designed to perform a preliminary alignment of chemical data obtained by gas chromatography. It was created to facilitate the comparison of multiple samples. The alignment algorithm is based on the comparison between each retention time, the following retention time in the same sample and its closest retention times in other samples. GCAligner is a java executable software running on any operating system. The input data file and the single output file containing the align data set are text files with tab delimited pieces of information.
See the software manual for further details.
::DEVELOPER
Simon Dellicour and Thomas Lecocq @ Evolutionary Biology & Ecology, Université Libre de Bruxelles
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:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
