Jalview is a free protein, RNA and DNA sequence visualisation program (http://www.jalview.org). In this tutorial, how to use the various analysis tools in Jalview for calculating and viewing trees from a sequence alignment are demonstrated.
http://www.jalview.org/ tutorial/alignment.fa
Jalview can calculated trees from distance matrices determined from % identity, feature similarity, PAM250 or BLOSUM 62 score using either Average Distance or Neighbour Joining algorithms. The tree can be divided to groups and these groups can be used to reorder the sequence alignment. A tree can be calculated from a subsection of the alignment. The appearance of the tree can be customized and exported as a Newick file, or saved as EPS or PNG file. Various ways that the tree viewer and groupings can be used to explore the similarities and difference in the alignment are discussed.
The sequence located at http://www.jalview.org/ tutorial/alignment.fa was used in the video. This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/document...). Other Jalview training videos can be viewed at in the training section of the web site (http://www.jalview.org/training/Train...).
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: (i) multiple sequence alignment (MSA), (ii) tree calculations and principle component analysis (PCA); (iii) consensus, conservation, and functional site analysis; (iv) secondary structure and disorder predictions; (v) visualisation of 3D structure.
Jalview was developed in Geoff Barton's group (http://www.compbio.dundee.ac.uk) in School of Life Sciences (http://www.lifesci.dundee.ac.uk ) at the University of Dundee (http://www.dundee.ac.uk). The team have also developed software JPRED (http://www.compbio.dundee.ac.uk/www-j...) and JABAWS (http://www.compbio.dundee.ac.uk/jabaws).
Video production by Dr Suzanne Duce, School of Life Sciences, University of Dundee
