TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

B.T.F. Alako, D. Rainey, H. Nijveen, J.A.M. Leunissen

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)


Phylogenetic analysis and examination of protein domains allow accurate genome annotation and are invaluable to study proteins and protein complex evolution. However, two sequences can be homologous without sharing statistically significant amino acid or nucleotide identity, presenting a challenging bioinformatics problem. We present TreeDomViewer, a visualization tool available as a web-based interface that combines phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences and generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. Thereby it makes use of existing domain prediction tools such as InterProScan. TreeDom Viewer adopts an evolutionary perspective on how domain structure of two or more sequences can be aligned and compared, to subsequently infer the function of an unknown homolog. This provides insight into the function assignment of, in terms of amino acid substitution, very divergent but yet closely related family members. Our tool produces an interactive scalar vector graphics image that provides orthological relationship and domain content of proteins of interest at one glance. In addition, PDF, JPEG or PNG formatted output is also provided. These features make TreeDomViewer a valuable addition to the annotation pipeline of unknown genes or gene products
Original languageEnglish
Pages (from-to)W104-W109
JournalNucleic acids research
Publication statusPublished - 2006


  • sequence
  • predictions
  • recognition
  • gene


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