:: DESCRIPTION
SINA (SILVA Incremental Aligner) will align and optionally taxonomically classify your rRNA gene sequences.
::DEVELOPER
The SILVA ribosomal RNA database project
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.
Pruesse E, Peplies J, Glöckner FO.
Bioinformatics. 2012 Jul 15;28(14):1823-9. doi: 10.1093/bioinformatics/bts252.
:: DESCRIPTION
KMAD was designed to align intrinsically disordered (aka natively unfolded) proteins for the HOPE mutation analysis server.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
KMAD: Knowledge based multiple sequence alignment for intrinsically disordered proteins.
Lange J, Wyrwicz LS, Vriend G.
Bioinformatics. 2015 Nov 14. pii: btv663.
:: DESCRIPTION
GenePainter is a standalone tool for mapping gene structures onto protein multiple sequence alignments (MSA). Gene structures, as provided by WebScipio, are aligned with respect to the exact positions of the introns (down to nucleotide level) and intron phase. Output can be viewed in various formats, ranging from plain text to graphical output formats.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Mühlhausen, M. Hellkamp & M. Kollmar (2014)
GenePainter 2.0 resolves the taxonomic distribution of intron positions.
Bioinformatics, pii: btu798
Björn Hammesfahr †, Florian Odronitz †, Stefanie Mühlhausen, Stephan Waack & Martin Kollmar (2013)
GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures.
BMC Bioinformatics 14, 77.
:: DESCRIPTION
PRRN is an implementation of the randomized iterative strategy for multiple sequence alignment. Prrn accepts either nucleotide or protein sequences. Prrn repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MSARC is a graph-clustering based algorithm that solves the multiple sequence alignment problem without guide-trees.
:: DEVELOPER
Computational and Systems Biology Group at the Faculty of Mathematics, Informatics and Mechanics, University of Warsaw
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Algorithms Mol Biol. 2014 Apr 16;9:12. doi: 10.1186/1748-7188-9-12. eCollection 2014.
MSARC: Multiple sequence alignment by residue clustering.
Modzelewski M, Dojer N.
:: DESCRIPTION
MSAProbs is a new and practical multiple alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Furthermore, MSAProbs is optimized for multi-core CPUs by employing a multi-threaded design, leading to a competitive execution time compared to other aligners.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities“.
Bioinformatics, 2010, 26(16): 1958 -1964
:: DESCRIPTION
Wasabi is a tool for visualisation and manipulation of rich MSAs and a graphical interface to command-line programs.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
Veidenberg A, Medlar A, Löytynoja A.
Mol Biol Evol. 2016 Apr;33(4):1126-30. doi: 10.1093/molbev/msv333.
:: DESCRIPTION
The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MSAViewer: interactive JavaScript visualization of multiple sequence alignments.
Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis S, Rost B, Goldberg T.
Bioinformatics. 2016 Jul 13. pii: btw474.
:: DESCRIPTION
LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an alignment in a revealing way.
::DEVELOPER
Lawrence-Dill Plant Informatics and Computation Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2004 Aug 12;20(12):1977-9. Epub 2004 Mar 25.
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference.
Lawrence CJ1, Zmasek CM, Dawe RK, Malmberg RL.
:: DESCRIPTION
KalignP is a modification to Kalign2, so that it accepts externally supplied position specific gap penalties.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jun 15;27(12):1702-3. doi: 10.1093/bioinformatics/btr235. Epub 2011 Apr 19.
KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.
Shu N1, Elofsson A.
