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The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. Expand
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available. Expand
Clustal W and Clustal X version 2.0
SUMMARY The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the futureExpand
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality. Expand
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
A new method for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives but avoids the most serious pitfalls caused by the greedy nature of this algorithm. Expand
Multiple sequence alignment with the Clustal series of programs
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of theExpand
Multiple sequence alignment with Clustal X.
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of allExpand
Multiple Sequence Alignment Using ClustalW and ClustalX
The protocols in this unit discuss how to use ClustalX and ClUSTalW to construct an alignment, and create profile alignments by merging existing alignments. Expand
Using CLUSTAL for multiple sequence alignments.
It is argued that using one weight matrix and two gap penalties is too simplistic to be of general use in the most difficult cases and a large number of new parameters designed primarily to help encourage gaps in loop regions are replaced. Expand