:: DESCRIPTION
CONSAN is a software of pairwise RNA structural alignment, both unconstrained and constrained on alignment pins.
::DEVELOPER
Robin Dowell, Eddy lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dowell, RD and Eddy, SR.
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
BMC Bioinformatics 2006, 7:400 .
:: DESCRIPTION
FastPairMI is a new software implementation for more efficiently computing the mutual information for all pairs of genes from gene expression microarrays.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Qiu P, Gentles AJ, Plevritis SK.
Fast calculation of pairwise mutual information for gene regulatory network reconstruction.
Comput Methods Programs Biomed. 2009 May;94(2):177-80. doi: 10.1016/j.cmpb.2008.11.003. Epub 2009 Jan 22. PMID: 19167129.
:: DESCRIPTION
CubeX calculates haplotype frequencies using the exact solution to the cubic equation rather than an iterative approach.
::DEVELOPER
Tom Gaunt’s group in the MRC IEU
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gaunt TR, Rodríguez S, Day IN.
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool ‘CubeX’.
BMC Bioinformatics. 2007 Nov 2;8:428.
:: DESCRIPTION
GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps.
GapMis is a tool for pairwise sequence alignment with a single gap.
GapMis-OMP is the OpenMP-based version of GapMis.
libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
GapsMis , GapMis , GapMis-OMP , libgapmis
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.
libgapmis: extending short-read alignments.
Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.
GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.
Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.
Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler.
Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library
:: DESCRIPTION
NW is an implementation of the Needleman and Wunsch dynamic programming sequence alignment algorithm. It reads PIR format sequence files and reports sequence similarity calculated in a number of different ways. Optionally it can generate a PIR format alignment file.
::DEVELOPER
Andrew C.R. Martin’s Bioinformatics Group at UCL
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
YAP (Yet Another Alignment Program) have the possibility of aligning two sequences of amino acids taking into account different properties, namely secondary structures, transmembranicity etc.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SNPduo is designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data between any two individuals. It has been designed based on data exported from Affymetrix CNAT 4.0 or Illumina Beadstudio, as well as data downloaded from the HapMap project. However, provided that the data is formatted correctly SNPduoWeb can analyze any SNP data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2009 Aug 21;4(8):e6711. doi: 10.1371/journal.pone.0006711.
Visualization of shared genomic regions and meiotic recombination in high-density SNP data.
Roberson ED, Pevsner J.
:: DESCRIPTION
The LnLCorr package is designed to detect pairwise coevolutionary among residues in a set of proteins using likelihood ratio tests.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang ZO, Pollock DD:
Coevolutionary patterns in cytochrome coxidase subunit I depend on structural and functional context.
J Mol Evol 2007, 65(5):485-495
:: DESCRIPTION
GS-Aligner that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods.
::DEVELOPER
Chun-Chieh Shih and Wen-Hsiung Li
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations
Chun-Chieh Shih and Wen-Hsiung Li
Mol Biol Evol (2003) 20 (8): 1299-1309.
:: DESCRIPTION
PALS (Pairwise Aligner for Long Sequences)is public domain software that finds local alignments of long DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
R.C. Edgar and E.W. Myers
PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158
