RAMACO – Compute Rare Maximal Exact Matches between Multiple Sequences

RAMACO

:: 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

Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Please contact Stefan Kurtz, if you are interested to obtain a version.

:: 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.

Squint 1.02 – Multiple Sequence Alignment Editor

Squint 1.02

:: 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

  • Windows / MacOsX / Linux

:: DOWNLOAD

 Squint

:: MORE INFORMATION

Citation:

Goode, M. and Rodrigo, A. G., (2007),
SQUINT: A multiple alignment program and editor.,
Bioinformatics 23:1553-1555.

Topali 2.5 r391 – Statistical & Evolutionary Analysis of Multiple Sequence Alignments

Topali 2.5 r391

:: DESCRIPTION

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.

::DEVELOPER

Information & Computational Sciences, The James Hutton Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 Topali

:: MORE INFORMATION

Citation

Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008),
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops,
Bioinformatics 25 (1), 126-127.

PROMALS3D – Multiple Sequence and Structure Alignment Server

PROMALS3D

:: 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

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • C++ Compiler
  • python
  • awk

:: DOWNLOAD

 PROMALS3D

:: 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.

Parallel T-Coffee 1.914 – Parallel Multiple Sequence Aligner based on TCoffee

Parallel T-Coffee 1.914

:: 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

Aluru HPC Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

 Parallel T-Coffee

:: 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.

CONTRAST 1.0 – Multiple Sequence de novo Gene Predictor

CONTRAST 1.0

:: 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

  • Linux

:: DOWNLOAD

 CONTRAST

:: 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.

CHROMA 1.0 – Annotated Multiple Sequence Alignments

CHROMA 1.0

:: 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

Llew Goodstadt

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • MS Word

:: DOWNLOAD

 CHROMA for win ; for Linux

:: 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.

Align-m 2.3 – Multiple Sequence Alignment

Align-m 2.3

:: 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

  • Windows/ Linux

:: DOWNLOAD

 Align-m

:: 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.