RAMACO is a software tool for computing rare maximal exact matches between multiple sequences. A rare match between k sequences S1,…,Sk is a string that occurs at most ti-times in the sequence Si, where the ti > 0 are user-defined thresholds.
The algorithm implemented in Ramaco is based on enhanced suffix arrays. First, the enhanced suffix array of one of the sequences (the reference sequence) is built and then the other sequences are matched separately against this enhanced suffix array. Second, the resulting pairwise exact matches are combined to multiple exact matches. Ramaco is very fast and space efficient, and can even process sets of mammalian chromosomes.
Topali (tree TOPology-related analysis of ALignments Interface) is a software for statistical and evolutionary analysis of multiple sequence alignments.The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.
PROMALS3D (PROfile Multiple Alignment with predicted Local Structures and 3D constraints) constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
Parallel T-Coffee (PTC) is the first parallel implementation of the TCoffee multiple sequence alignment tool. It has been developed to overcome main limitations of the original method. It is based on the MPI and RMA mechanisms, and it can be run on distributed memory clusters. PTC supports a majority of options provided by TCoffee 3.79, including the 3D-Coffee mode. It can be used to align data sets consisting of hundreds of proteins in reasonable time limits.
CONTRAST predicts protein-coding genes from a multiple genomic alignment using a combination of discriminative machine learning techniques. A two-stage approach is used, in which output from local classifiers is combined with a global model of gene structure. CONTRAST is trained using a novel procedure designed to maximize expected coding region boundary detection accuracy.
CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication.CHROMA takes your aligned multiple sequence data, annotates residues according to a consensus and displays the alignment using different font formats (text and background colours, bold and italic).
Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks
– Multiple sequence alignment
– Include extra information to guide the sequence alignment
– Multiple structure alignment
– Homology modeling by (iteratively) combining sequence and structure alignment data
– ‘Filtering’ of Blast or other pairwise alignments
– Combining many alignments into 1 consensus
– Multiple genome alignment (can cope with rearrangements)