:: DESCRIPTION
PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.
RNA secondary structural alignment with conditional random fields.
Sato K, Sakakibara Y.
:: DESCRIPTION
AlphaMALIG (ALPHAbet Multiple ALIGnment) is a tool which allows you to align many but no more than 200 sequences. These sequences will be formed by characters of a finite alphabet.
::DEVELOPER
the Algorithmics and Genetics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
deepBlockAlign is a tool for aligning RNA-seq profiles of read block patterns.The analysis starts from closely spaced blocks of mapped reads, which we call block groups.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Langenberger, D., Pundhir, S., Ekstrøm, C.T., Stadler, P.F., Hoffmann, S., and Gorodkin, J. (2011).
deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns.
Bioinformatics. 2012 Jan 1;28(1):17-24. doi: 10.1093/bioinformatics/btr598
:: DESCRIPTION
ArkMAP is a desktop application that allows users to draw and align genetic maps.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013 Aug 13;14:246. doi: 10.1186/1471-2105-14-246.
ArkMAP: integrating genomic maps across species and data sources.
Paterson T, Law A.
:: DESCRIPTION
DualAligner performs dual network alignment, in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments.
::DEVELOPER
Computational Systems Biology Research Group(COSBY)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 May 28. pii: btu358. [Epub ahead of print]
DualAligner: A Dual Alignment-based Strategy to Align Protein Interaction Networks.
Seah BS1, Bhowmick SS2, Dewey CF Jr3.
:: DESCRIPTION
LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
::DEVELOPER
Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.
:: DESCRIPTION
SMALT efficiently aligns DNA sequencing reads with genomic reference sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
AREM (Aligning reads by Expectation-Maximization) is a peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
J Comput Biol. 2011 Nov;18(11):1495-505. Epub 2011 Oct 28.
AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.
:: DESCRIPTION
ASAP(Allele-specific Alignment Pipeline) is a program to align a sequencing file to two genomes at the same time. This can be useful to detect allelic imbalances in samples which are of different genetic origin. Examples would be studying imprinted regions in ChIP-Seq or RNA-Seq experiments, or genomic interactions (e4C) in mouse strains with a mixed genetic background.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
