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Phylogenetic analysis of BLAST results

Part 4. Bioinformatics

4.4. Comparative Analysis and Phylogeny

Short Specialist Review

  1. Fiona S. L. Brinkman

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g404302

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Brinkman, F. S. L. 2005. Phylogenetic analysis of BLAST results. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.4:47.

Author Information

  1. Simon Fraser University, Burnaby, BC, Canada

Publication History

  1. Published Online: 15 JUL 2005


BLAST (Basic Local Alignment Search Theorem) is one of the most elegant, and widely used bioinformatics analysis developed to date. Like many bioinformatic analyses, BLAST uses evolutionary theory as the basis for its assumptions. Therefore, an understanding of evolutionary theory is critical to the appropriate interpretation, and further analysis, of BLAST results. Viewing essentially one-dimensional BLAST analysis from the perspective of a two-dimensional phylogenetic analysis has a number of benefits including more accurate identification of the true “top hit”, delineation of gene families, identification of true homologs, and improved functional assignment of orthologs and paralogs. Performing such phylogenetic analyses has become easier, now that semiautomated methods have been developed that permit rough phylogenetic overviews of the data. However, it should be emphasized that phylogenetic analysis must often be customized for a given experiment or research question. Such issues are relevant not only to the further analysis of a BLAST output, but also to similar analyses of outputs from other widely used algorithms for rapid database search. Critical analysis of results is becoming increasingly important as sequence databases increase in both size and complexity – and as we begin to understand that even these large sequence databases are only scratching the surface of the true complexity and variety of sequences that exist in nature.


  • BLAST;
  • FASTA;
  • BLAT;
  • phylogenetic analysis;
  • phylogenetics;
  • evolution;
  • evolutionary analysis;
  • bioinformatics;
  • gene families;
  • homologs;
  • orthologs;
  • paralogs