:: DESCRIPTION
FOGSAA aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sci Rep. 2013;3:1746. doi: 10.1038/srep01746.
FOGSAA: Fast Optimal Global Sequence Alignment Algorithm.
Chakraborty A1, Bandyopadhyay S.
:: DESCRIPTION
FALP calculates the statistical parameters in the modified Gumbel distribution for gapped alignment with frameshifts.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ALP & FALP: C++ Libraries for pairwise local alignment E-values.
Sheetlin S, Park Y, Frith MC, Spouge JL.
Bioinformatics. 2015 Oct 1. pii: btv575.
Frameshift alignment: statistics and post-genomic applications.
Sheetlin SL, Park Y, Frith MC, Spouge JL.
Bioinformatics. 2014 Aug 28. pii: btu576.
:: DESCRIPTION
Oculus is a bioinformatic algorithm designed to increase sequence alignment speed for redundant input. It acts as a wrapper around any existing alignment algorithm capable of producing SAM-formatted output.
::DEVELOPER
The Michigan Center for Translational Pathology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
BMC Bioinformatics. 2012 Nov 13;13:297. doi: 10.1186/1471-2105-13-297.
Oculus: faster sequence alignment by streaming read compression.
Veeneman BA1, Iyer MK, Chinnaiyan AM.
:: DESCRIPTION
GPU-BLAST is an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). The implementation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interface while producing identical results. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Panagiotis D. Vouzis and Nikolaos V. Sahinidis,
“GPU-BLAST: using graphics processors to accelerate protein sequence alignment,”
Bioinformatics, 2011 Vol. 27, no. 2, pages 182-188,
:: DESCRIPTION
Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2006 Sep 1;22(17):2168-70. Epub 2006 Jul 4.
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.
Mokdad A, Leontis NB.
:: DESCRIPTION
SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences.
::DEVELOPER
Pacific Biosciences of California, Inc
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Integr. 2011 Dec 20;2:10. doi: 10.1186/2041-9414-2-10.
Direct detection and sequencing of damaged DNA bases.
Clark TA, Spittle KE, Turner SW, Korlach J.
:: DESCRIPTION
elPrep is a high-performance tool for preparing .sam/.bam/.cram files for variant calling in sequencing pipelines.It can be used as a drop-in replacement for SAMtools/Picard, and was extensively tested with different pipelines for variant analysis with GATK.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.
elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.
Herzeel C, Costanza P, Decap D, Fostier J, Reumers J
:: DESCRIPTION
SAT is a software to teach about sequence alignment methods based on dynamic programming such as Smith – Waterman (Local) and Needleman – Wunsch (Global).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jul 1;26(13):1664-5. doi: 10.1093/bioinformatics/btq252. Epub 2010 May 14.
Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.
Ibarra IL1, Melo F.
:: DESCRIPTION
PhySamp is a package dedicated to phylogenetic sampling. It samples a sequence alignment according to its corresponding phylogenetic tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Dutheil JY1,2, Figuet E3.
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.
BMC Bioinformatics. 2015 Jun 9;16:190.
:: DESCRIPTION
ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families.It reads a variety of file formats directly from the database web-sites including: PDB, chemical, electron density maps, sequence and alignment files. ICM-Browser provides a rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.
When you purchase the license ICM-Browser will become ICM-Browser-Pro.ICM-Browser-Pro is a high quality visualizer and annotator for three dimensional molecular structures, sequences, alignments, chemical spreadsheets and biological data. It allows you to read data from multiple file formats, annotate the data, and write multi-slide documents in a single small cross-platform file. ICM Browser Pro is well suited for creating, storing and sharing structural, biological and chemical information. The files can then be opened and viewed with the free ICM Browser.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
