Adding unaligned sequences into an existing alignment using MAFFT and LASTKATOH, Kazutaka; FRITH, Martin C.Bioinformatics (Oxford. Print). 2012, Vol 28, Num 23, pp 3144-3146, issn 1367-4803, 3 p.Article

A probabilistic measure for alignment-free sequence comparisonPHAM, Tuan D; ZUEGG, Johannes.Bioinformatics (Oxford. Print). 2004, Vol 20, Num 18, pp 3455-3461, issn 1367-4803, 7 p.Article

Multi-objective pairwise RNA sequence alignmentTANEDA, Akito.Bioinformatics (Oxford. Print). 2010, Vol 26, Num 19, pp 2383-2390, issn 1367-4803, 8 p.Article

Cyclic sequence alignments: Approximate versus optimal techniquesMOLLINEDA, R. A; VIDAL, E; CASACUBERTA, F et al.International journal of pattern recognition and artificial intelligence. 2002, Vol 16, Num 3, pp 291-299, issn 0218-0014Article

Parallelization of the MAFFT multiple sequence alignment programKATOH, Kazutaka; TOH, Hiroyuki.Bioinformatics (Oxford. Print). 2010, Vol 26, Num 15, pp 1899-1900, issn 1367-4803, 2 p.Article

RDP2: recombination detection and analysis from sequence alignmentsMARTIN, D. P; WILLIAMSON, C; POSADA, D et al.Bioinformatics (Oxford. Print). 2005, Vol 21, Num 2, pp 260-262, issn 1367-4803, 3 p.Article

Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problemsGRASSO, Catherine; LEE, Christopher.Bioinformatics (Oxford. Print). 2004, Vol 20, Num 10, pp 1546-1556, issn 1367-4803, 11 p.Article

Strategies for multiple sequence alignmentNICHOLAS, Hugh B; ROPELEWSKI, Alexander J; DEERFIELD, David W et al.BioTechniques. 2002, Vol 32, Num 3, pp 572-591, issn 0736-6205, 13 p.Article

Distributed BLAST in a grid computing contextBAYER, Micha M; SINNOTT, Richard.Lecture notes in computer science. 2005, pp 241-252, issn 0302-9743, isbn 3-540-29104-0, 1Vol, 12 p.Conference Paper

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstructionWESTESSON, Oscar; BARQUIST, Lars; HOLMES, Ian et al.Bioinformatics (Oxford. Print). 2012, Vol 28, Num 8, pp 1170-1171, issn 1367-4803, 2 p.Article

Measuring the distance between multiple sequence alignmentsBLACKBURNE, Benjamin P; WHELAN, Simon.Bioinformatics (Oxford. Print). 2012, Vol 28, Num 4, pp 495-502, issn 1367-4803, 8 p.Article

Jalview Version 2-a multiple sequence alignment editor and analysis workbenchWATERHOUSE, Andrew M; PROCTER, James B; MARTIN, David M. A et al.Bioinformatics (Oxford. Print). 2009, Vol 25, Num 9, pp 1189-1191, issn 1367-4803, 3 p.Article

Multiperm : shuffling multiple sequence alignments while approximately preserving dinucleotide frequenciesANANDAM, Parvez; TORARINSSON, Elfar; RUZZO, Walter L et al.Bioinformatics (Oxford. Print). 2009, Vol 25, Num 5, pp 668-669, issn 1367-4803, 2 p.Article

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignmentPATEN, Benedict; HERRERO, Javier; BEAL, Kathryn et al.Bioinformatics (Oxford. Print). 2009, Vol 25, Num 3, pp 295-301, issn 1367-4803, 7 p.Article

Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisonsMARGULIES, Elliott H; CHEN, Christina W; GREEN, Eric D et al.Trends in genetics (Regular ed.). 2006, Vol 22, Num 4, pp 187-193, issn 0168-9525, 7 p.Article

Bridging expressed sequence alignments through targeted cDNA sequencingHANQING XIE; DIBER, Alex; GILL-MORE, Raveh et al.Genomics (San Diego, Calif.). 2004, Vol 83, Num 4, pp 572-576, issn 0888-7543, 5 p.Article

Where did the BLOSUM62 alignment score matrix come from?EDDY, Sean R.Nature biotechnology. 2004, Vol 22, Num 8, pp 1035-1036, issn 1087-0156, 2 p.Article

Improvement of the Needleman-Wunsch algorithmZHIHUA DU; FENG LIN.Lecture notes in computer science. 2004, pp 792-797, issn 0302-9743, isbn 3-540-22117-4, 6 p.Conference Paper

KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2NANJIANG SHU; ELOFSSON, Arne.Bioinformatics (Oxford. Print). 2011, Vol 27, Num 12, pp 1702-1703, issn 1367-4803, 2 p.Article

PatMaN : rapid alignment of short sequences to large databasesPRÜFER, Kay; STENZEL, Udo; DANNEMANN, Michael et al.Bioinformatics (Oxford. Print). 2008, Vol 24, Num 13, pp 1530-1531, issn 1367-4803, 2 p.Article

ProfDistS : (profile-) distance based phylogeny on sequence-structure alignmentsWOLF, Matthias; RUDERISCH, Benjamin; DANDEKAR, Thomas et al.Bioinformatics (Oxford. Print). 2008, Vol 24, Num 20, pp 2401-2402, issn 1367-4803, 2 p.Article

An algorithm for locating nonoverlapping regions of maximum alignment scoreKANNAN, S. K; MYERS, E. W.SIAM journal on computing (Print). 1996, Vol 25, Num 3, pp 648-662, issn 0097-5397Article

Local RNA structure alignment with incomplete sequenceKOLBE, Diana L; EDDY, Sean R.Bioinformatics (Oxford. Print). 2009, Vol 25, Num 10, pp 1236-1243, issn 1367-4803, 8 p.Article

ViTO: tool for refinement of protein sequence-structure alignmentsCATHERINOT, Vincent; LABESSE, Gilles.Bioinformatics (Oxford. Print). 2004, Vol 20, Num 18, pp 3694-3696, issn 1367-4803, 3 p.Article

Parallelized multiple alignmentKLEINJUNG, Jens; DOUGLAS, Nigel; HERINGA, Jaap et al.Bioinformatics (Oxford. Print). 2002, Vol 18, Num 9, pp 1270-1271, issn 1367-4803Article