:: DESCRIPTION
RL-CSA is a tool for regular-language constrained pairwise global sequence alignment
::DEVELOPER
Michal Ziv-Ukelson’s Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kucherov, G., Pinhas, T., Ziv-Ukelson, M.:
Regular Language Constrained Sequence Alignment Revisited,
J Comput Biol. 2011 May;18(5):771-81.
:: DESCRIPTION
Formatt is a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments.
::DEVELOPER
Bioinformatics and Computational Biology Research Group, Tufts University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2012 Oct 6;13:259. doi: 10.1186/1471-2105-13-259.
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.
Daniels NM, Nadimpalli S, Cowen LJ.
:: DESCRIPTION
InterEvol PyMOL is a pymol plugin to perform structure-oriented exploration of the sequence alignments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Jan;40(Database issue):D847-56. doi: 10.1093/nar/gkr845. Epub 2011 Nov 3.
InterEvol database: exploring the structure and evolution of protein complex interfaces.
Faure G1, Andreani J, Guerois R.
:: DESCRIPTION
SBAL is intended for multiple protein sequence alignments guided by secondary structure elements. The program provides automatic and semi-automatic alignment features, and also possesses manual editing capabilities.
::DEVELOPER
Hofmann Laboratory, Eskitis Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang, C.K., Broder, U., Weeratunga, S.K., Gasser, R.B., Loukas, A., Hofmann, A. (2012)
SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.
Bioinformatics 28, 1026-1027.
:: DESCRIPTION
MO-SAStrE proposes a multiobjective genetic approach that takes advantage of three different objectives: STRIKE score (based on structural information), totally conserved (TC) columns and percentage of non-gaps. Additionally, this algorithm also applies a novel codification of individuals as well as efficient mutation and crossover operators. This algorithm is implemented through the well-known multiobjective non-dominated sorting genetic algorithm (NSGA-II) approach.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Sep 1;29(17):2112-21. doi: 10.1093/bioinformatics/btt360. Epub 2013 Jun 21.
Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.
Ortuño FM1, Valenzuela O, Rojas F, Pomares H, Florido JP, Urquiza JM, Rojas I.
:: DESCRIPTION
ProPIP is a Multiple Sequence Alignment inference software that implements the Poisson Indel Process (Bouchard-Côté & Jordan, PNAS, 2013) in the Maximum Likelihood framework.
::DEVELOPER
Applied Computational Genomics Team
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Maiolo M, Gatti L, Frei D, Leidi T, Gil M, Anisimova M.
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process.
BMC Bioinformatics. 2021 Oct 24;22(1):518. doi: 10.1186/s12859-021-04442-8. PMID: 34689750; PMCID: PMC8543915.
:: DESCRIPTION
ADEPT is a GPU accelerated sequence alignment library for short DNA reads and protein sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Awan MG, Deslippe J, Buluc A, Selvitopi O, Hofmeyr S, Oliker L, Yelick K.
ADEPT: a domain independent sequence alignment strategy for gpu architectures.
BMC Bioinformatics. 2020 Sep 15;21(1):406. doi: 10.1186/s12859-020-03720-1. PMID: 32933482; PMCID: PMC7493400.
:: DESCRIPTION
Strap (STRucture-based Sequence Alignment Program) aligns proteins by sequence and 3D-structure.Strap supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
HotSwap for bioinformatics: a STRAP tutorial.
Gille C, Robinson PN.
BMC Bioinformatics. 2006 Feb 9;7:64.
:: DESCRIPTION
PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Jul 1;28(13):1684-91. doi: 10.1093/bioinformatics/bts198. Epub 2012 Apr 23.
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A1, Vilella AJ, Goldman N.
:: DESCRIPTION
SiteSampler is a Java application that can sample the sites of a sequence alignment to produce replicate data sets.
::DEVELOPER
the Molecular Ecology, Evolution, and Phylogenetics (MEEP) Lab in the School of Biological Sciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ho SYW, and Lanfear R (2010)
Improved characterization of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks.
Mitochondrial DNA, 21: 138-146.
