:: DESCRIPTION
Squint is an advanced alignment tool. It brings together algorithmic alignment of molecular sequences, with human editing. It is an extension of the alignment editor available in Pebble.
::DEVELOPER
the New Zealand Bioinformatics Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Goode, M. and Rodrigo, A. G., (2007),
SQUINT: A multiple alignment program and editor.,
Bioinformatics 23:1553-1555.
:: DESCRIPTION
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.
::DEVELOPER
Prof. Srinivas Aluru Research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J. Zola, X. Yang, S. Rospondek, S. Aluru
Parallel T-Coffee: A Parallel Multiple Sequence Aligner
In Proc. of ISCA PDCS-2007, pp. 248-253, 2007.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ohlebusch, E. and Kurtz, S.
Space efficient computation of rare maximal exact matches between multiple sequences
J. Comp. Biol. 15(4):357-377, 2008.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PROMALS3D: a tool for multiple sequence and structure alignment.
Jimin Pei, Bong-Hyun Kim and Nick V. Grishin.
Nucleic Acids Res. 2008 36(7):2295-2300.
:: DESCRIPTION
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.
::DEVELOPER
Chuong Do (chuongdo@cs.stanford.edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gross SS, Do CB, Sirota M, Batzoglou S.
CONTRAST: A Discriminative, Phylogeny-free Approach to Multiple Informant De Novo Gene Prediction.
Genome Biology, submitted.
:: DESCRIPTION
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).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Leo Goodstadt and Chris P. Ponting
CHROMA: consensus-based colouring of multiple alignments for publication.
Bioinformatics. 2001 Sep;17(9):845-6.
:: DESCRIPTION
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)
::DEVELOPER
Vrije Universiteit Brussel – Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Van Walle I, Lasters I, Wyns L.
Align-m–a new algorithm for multiple alignment of highly divergent sequences.
Bioinformatics. 2004 Jun 12;20(9):1428-35. Epub 2004 Feb 12.
