Optimizing substitution matrix choice and gap parameters for sequence alignment

This publication has 27 references indexed in Scilit:

• Automatic Parameter Learning for Multiple Local Network Alignment
  Journal of Computational Biology, 2009
• Clustal W and Clustal X version 2.0
  Bioinformatics, 2007
• Multiple alignment of protein sequences with repeats and rearrangements
  Nucleic Acids Research, 2006
• MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information
  Nucleic Acids Research, 2006
• Parametric Alignment of Drosophila Genomes
  PLoS Computational Biology, 2006
• MAFFT version 5: improvement in accuracy of multiple sequence alignment
  Nucleic Acids Research, 2005
• MUSCLE: multiple sequence alignment with high accuracy and high throughput
  Nucleic Acids Research, 2004
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
  Nucleic Acids Research, 1994
• Parametric optimization of sequence alignment
  Algorithmica, 1994
• The rapid generation of mutation data matrices from protein sequences
  Bioinformatics, 1992