AMPS (Alignment of Multiple Protein Sequences) is a suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures. AMPS also implements flexible pattern matching and database scanning options. AMPS includes functions for running randomisations to estimate the significance of sequence similarities.
ParaAT (Parallel Alignment and back-Translation) is a parallel tool that parallelly constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.
ASH is a structure alignment program that has been developed for PDBj.
RASH Rapid ASH computes pair-wise alignments in under 1 second. RASH is generally sufficient if the structures are very similar.
GASH Genetic-algorithm ASH generates very accurate alignments in about twice the time as RASH. GASH is the best choice if the structures are only partially similar or if multiple solutions are required.
LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.
CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures.
ChromA (Chromatogram Alignment) provides the Dynamic Time Warping algorithm for the alignment of data from the domain of Gas- and Liquid-Chromatography Mass-Spectrometry. It uses additional constraints and can be configured to use different local functions to evaluate the similarity of mass spectra between chromatograms. It allows the definition of anchors, which are the positions of conserved compounds, constraining the alignment and providing a speedup. Furthermore, ChromA provides different visualizations of the alignment, as well as a textual format for further processing of chromatograms.