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<HTML>
<TITLE>Trees from Blocks</TITLE>
<H1><IMG ALIGN=MIDDLE SRC="/blocks/icons/blocks.xbm">About Trees from Blocks</H1>
<H3>Generation and Display of Trees from Related Sequences, Blocks, and Multiple Alignments</H3>
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.
<BR><P>
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 <A HREF="http://www2.ebi.ac.uk/clustalw/">EBI Clustal</A> or the <A HREF="http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html">BCM Search Launcher</A> multiple sequence alignment site for
global multiple alignments from which blocks are made, or use
<A HREF="/blocks/make_blocks.html">Block Maker</A> to make blocks directly. Clustal-generated alignments
are copied and pasted into the
<A HREF="/blocks/process_blocks.html">Multiple Alignment Processor</A> 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.
<A HREF="/blocks-bin/kidofwais.pl">Get Blocks</A> (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.
<HR>
<H3>How Trees are made</H3>
The neighbor-joining trees are made from the Block alignments using a routine in Clustal W
[<A HREF="ftp://ftp.ebi.ac.uk/pub/software">Clustal ftp site</A>].
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 <A HREF="clustal.txt">Clustal documentation</A> ).
<P>Clustal W versions 1.7+ will not make a tree with fewer than four
sequences.
<P>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.
<P>
The the drawgram program from the
<A HREF="http://evolution.genetics.washington.edu/phylip.html">PHYLIP</A>
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:
<PRE>
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
</PRE>
<P>
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):
<PRE>
Type: application/newick
Suffix: treefile, tre
Application: treetool %s
</PRE>
Tree display programs include
<A HREF="http://pbil.univ-lyon1.fr/software/njplot.html">NJplot</A>,
<A HREF="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">TreeView</A> and
<A HREF="http://magpie.bio.indiana.edu/IUBio-Software+Data/molbio/unix/GDE/treetool/">Treetool</A>.
<P>
<HR>
<A HREF="/blocks">Blocks home</A>
<HR>
<A href="contact.html">Contact us</A> <P>
Page last modified <MODIFICATION_DATE>Aug 1999</MODIFICATION_DATE>
</HTML>
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