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Strategies for Multiple Sequence Alignment
BioTechniques, 2002 We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence ...
Hugh B. Nicholas +2 more
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Using structure to explore the sequence alignment space of remote homologs. [PDF]
PLoS Computational Biology, 2011 Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate ...
Andrew Kuziemko +2 more
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BEAST: Bayesian evolutionary analysis by sampling trees [PDF]
, 2007 Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics ...
Drummond, Alexei J., Rambaut, Andrew
core +3 more sources
Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences
IEEE Access, 2019 The computational techniques for nucleic acid and protein sequence comparison reduce the extensive burden of molecular biologists. The sequence alignment is one of the main research areas in bioinformatics, and comparative genomics and proteomics lead us
Muhammad Ishaq +3 more
doaj +1 more source
bioRxiv, 2021 Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one alignment by some preferred method and use it in further analysis; however,
Robert C. Edgar
semanticscholar +1 more source
Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450 [PDF]
, 2006 Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection.
Arnold, Frances H. +5 more
core +1 more source
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
BMC Bioinformatics, 2004 BackgroundIn a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy
Robert C. Edgar
semanticscholar +1 more source
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
PLoS Biology, 2020 Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference.
J. Steenwyk +4 more
semanticscholar +1 more source
Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure [PDF]
, 2013 Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees.
Bakis, Yasin +11 more
core +2 more sources