The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

@article{Thompson1997TheCW,
  title={The CLUSTAL\_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.},
  author={J Drew Thompson and Toby J. Gibson and Fr{\'e}d{\'e}ric Plewniak and F Jeanmougin and Desmond G. Higgins},
  journal={Nucleic acids research},
  year={1997},
  volume={25 24},
  pages={
          4876-82
        }
}
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional… 

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References

SHOWING 1-10 OF 47 REFERENCES
A workbench for multiple alignment construction and analysis
TLDR
An interactive program, MACAW (Multiple Alignment Construction and Analysis Workbench), that allows the user to construct multiple alignments by locating, analyzing, editing, and combining “blocks” of aligned sequence segments.
DCSE, an interactive tool for sequence alignment and secondary structure research
TLDR
Although DCSE can be used on protein sequence alignments, it is especially targeted at the examination of RNA because it uses a different approach towards editing.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
TLDR
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.
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
TLDR
An algorithm is described for the systematic characterization of the physico-chemical properties seen at each position in a multiple protein sequence alignment that simplifies the analysis of multiple sequence data by condensing the mass of information present, and thus allows the rapid identification of substitutions of structural and functional importance.
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
SEAVIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEAVIEW is a sequence alignment editor allowing manual or
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.
  • O. Gotoh
  • Biology
    Journal of molecular biology
  • 1996
TLDR
The improvement in accuracy of alignments obtained by these iterative methods over pairwise or progressive method tends to increase with decreasing average sequence identity, implying that iterative refinement is more effective for the generally difficult alignment of remotely related sequences.
Improved sensitivity of profile searches through the use of sequence weights and gap excision
TLDR
The performance of the database searches is enhanced by using a sequence weighting scheme which assigns higher weights to more distantly related sequences based on branch lengths derived from phylogenetic trees and the BLOSUM62 residue comparison matrix.
CLUSTAL V: improved software for multiple sequence alignment
TLDR
The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added, the main new features are the ability to store and reuse old alignments and to calculate phylogenetic trees after alignment.
...
1
2
3
4
5
...