Results 51 to 60 of about 1,513,801 (381)

Reticular alignment: A progressive corner-cutting method for multiple sequence alignment

BMC Bioinformatics, 2010
Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table ...
Novák Ádám, Szabó Adrienn, Miklós István, Hein Jotun   +3 more
doaj   +1 more source

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

Nucleic Acids Research, 2002
A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques.
K. Katoh, K. Misawa, K. Kuma, T. Miyata
semanticscholar   +1 more source

Evolutionary distances in the twilight zone -- a rational kernel approach [PDF]

, 2010
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.
A Keller, A Löytynoja, A Stamatakis, B Chor, B Schölkopf, Benjamin Merget, C Cortes, C Daskalakis, CB Do, E Rivas, F Bemm, Florian Markowetz, Frank Förster, G Talavera, HH Otu, I Ulitsky, J Felsenstein, J Friedrich, J Hein, JL Thorne, JL Thorne, Jörg Schultz, KM Wong, LS Wang, M Höhl, M Höhl, M Mohri, M Mohri, M Wolf, MA Buchheim, MA Suchard, Matthias Wolf, MJ Bishop, MK Kuhner, MS Waterman, N Goldman, N Higham, R Durbin, RC Edgar, RF Doolittle, Roland F. Schwarz, S Roch, S Whelan, SR Eddy, T Mailund, T Müller, TH Ogden, V Levenshtein, W Fletcher, W Fletcher, Wayne Delport, William Fletcher   +51 more
core   +4 more sources

Developments in Algorithms for Sequence Alignment: A Review

Biomolecules, 2022
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately.
Jiannan Chao, Furong Tang, Lei Xu
doaj   +1 more source

Parameter advising for multiple sequence alignment [PDF]

BMC Bioinformatics, 2015
DeBlasio D, Kececioglu J.
europepmc   +4 more sources

MAFFT version 5: improvement in accuracy of multiple sequence alignment

Nucleic Acids Research, 2005
The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective ...
K. Katoh, K. Kuma, H. Toh, T. Miyata
semanticscholar   +1 more source

Alvira : comparative genomics of viral strains [PDF]

, 2007
The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large ...
Brodie, Chenna, E. Baranowski, Edgar, F. Enault, Ghedin, Lassmann, Lee, R. Fremez, T. Faraut, Zmasek   +10 more
core   +2 more sources

Recent developments in the MAFFT multiple sequence alignment program

Briefings Bioinform., 2008
The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002 ...
K. Katoh, H. Toh
semanticscholar   +1 more source

Multiple sequence alignment based on structural properties [PDF]

, 2010
A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences. Main idea behind multiple sequence alignment is to see the similarities between input sequences, to be able to make phylogenetic analysis and other ...
Gezici, Gizem, Meydan, C., Ozer, B., Sezerman, U.   +3 more
core   +1 more source

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Viruses, 2022
The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data.
Colin Young, Sarah Meng, Niema Moshiri
doaj   +1 more source