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).
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.
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
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.
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).
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.