# About Trees from Blocks

### Generation and Display of Trees from Related Sequences, Blocks, and Multiple Alignments

A set of blocks can also be used to construct and display a neighbor-joining tree for examination of possible subfamily relationships. Because blocks represent the most highly conserved regions of proteins, misaligned regions are avoided, and so trees from blocks should be of high quality. Bootstrap resampling percentages are supplied to aid in evaluating the significance of each branch.

Start with a set of related sequences or a multiple alignment in Blocks, Clustal or FASTA-alignment format. For a set of related sequences, get a ClustalW alignment using either the EBI Clustal or the BCM Search Launcher multiple sequence alignment site for global multiple alignments from which blocks are made, or use Block Maker to make blocks directly. Clustal-generated alignments are copied and pasted into the Multiple Alignment Processor window in Clustal (include the word 'CLUSTAL' from the heading) or FASTA-alignment format, and choose 'Submit the sequences'. The processor carves out blocks from fully-ungapped regions that are at least 10 residues wide and provides an automatic link for making a tree from the full set of blocks. Get Blocks (for Blocks Database entries) and Block Maker (which uses Motif or Gibbs sampling) provides blocks that are ready to go. In each case, there are links to various displays of neighbor-joining trees.

### How Trees are made

The neighbor-joining trees are made from the Block alignments using a routine in Clustal W [Clustal ftp site]. The Kimura correction for multiple substitutions is applied. If there are not too many sequences, 100 bootstrap values are calculated. The output from Clustal W is a tree file in Newick or New Hampshire format which can be read by most tree display programs. ( Excerpts from Clustal documentation ).

Clustal W versions 1.7+ will not make a tree with fewer than four sequences.

NOTE: Before attempting to display a tree, look at the Clustal W output by selecting [Data] format to check for error messages. Common problems that can cause Clustal W to fail are: non-unique sequence names (the first 10 characters of each name should be unique) and sequence title lines that start with ">P1;" which causes Clustal W to assume the sequences are in PIR format instead of FASTA format.

The the drawgram program from the PHYLIP package is used to format the tree for display. Resolution is calculated according to number of sequences in the tree using values that give satisfactory images viewed with NetScape on a Mac: Here are the drawgram parameters used:

         resolution = num_seqs * 25 + 50

         "X"          # X - 'X bitmap (XBM)'
         "N"          # N - No preview
         $resolution  # XBM horizontal resolution
         $resolution  # XBM vertical resolution
         "1"          # Tree growth, toggle to horizontal
         "2"          # Style of tree
         "P"          # P for Phenogram style
         "4"          # Angle of labels
         "90"         # labels 90 degrees to the tree
         "8"          # Stem-length/tree-depth
         "0"          # 0 stem won't show
         "Y"          # Y(es) to accept choices

The trees can also be displayed locally using any program that accepts input in Newick format, such as those listed below. To activate this feature in your browser (such as Netscape), enter these "helper application" parameters (substitute your application program for treetool):

    Type: application/newick
    Suffix:  treefile, tre
    Application:  treetool %s

Tree display programs include NJplot, TreeView and Treetool.

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Page last modified <MODIFICATION_DATE>Aug 1999</MODIFICATION_DATE>