This file describes how to create an image with our species tree.

First, we need to re-scale the tree in order to improve the readability.
We use a log-scale and make internal branches slightly smaller than final
ones:

more ensembl-compara/scripts/pipeline/species_tree_blength.nw | \
  perl -e 'my @a = split(/([\)\,])/, $_);
    foreach my $a (@a) {
      if ($a =~ /(.*\w\:)(\d\.\d+)(.*)/) {
        print $1, log(1.6+$2), $3; # final branches, make them slightly larger than...
      } elsif ($a =~ /(.*)(\d\.\d+)(.*)/) {
        print $1, log(1.2+$2), $3; # ... internal branches
      } else {
        print $a;
      }
    }' -n > rescaled_tree.nw

more ensembl-compara/scripts/pipeline/species_tree_blength.nh | \
  perl -e '$_ =~ s/\)\w+/\)/g;
    $_ =~ s/\?\w+/XXXXXXXXXXX/g;
    my @a = split(/([\)\,])/, $_);
    foreach my $a (@a) {
      if ($a =~ /(.*\w\:)(\d\.\d+)(.*)/) {
        print $1, log(1.6+$2), $3; # final branches, make them slightly larger than...
      } elsif ($a =~ /(.*)(\d\.\d+)(.*)/) {
        print $1, log(1.2+$2), $3; # ... internal branches
      } else {
        print $a;
      }
    }' -n > rescaled_tree.nw

Open Dendroscope. Load the file and select the Radial Phylogram (Ctrl+7).
- In the view menu, deselect "Sparse labels" and choose "Radial labels".
- Adjust the tree, by rotating it left or right.
- Remove species not in e! by selecting them and Ctrl+Backspace
- Rotate nodes with Ctrl+Shift+T if you wish (Cionas tend to get on the internal side after removing mosquitoes)

If you want to let Dendroscope load the figures automatically, do:
cd ~/src/public-plugins/ensembl/htdocs/img/species
mkdir ~/tmp/species_tree_imgs
ls thumb_* | sed -e 's/thumb_//' | while read i; do \
  cp thumb_$i ~/tmp/species_tree_imgs/$i; done
And go to Options -> Load Taxon Images...
You can change the size of the images in Options -> Set Image Size...

Save the file as a PDF or an SVG.

Don't forget to cite:
D.H. Huson, D. C. Richter, C. Rausch, T. Dezulian, M. Franz and R. Rupp, Dendroscope- An interactive viewer for large phylogenetic trees, BMC Bioinformatics 8:460, 2007

You can do that by modifying the SVG file with a text editor. Try to add
    <text id="dendroscoperef" fill="#303030" fill-opacity="1" font-family="Sans Serif" font-size="10pt"       x="200pt" y="500pt">
Image obtained using Dendroscope (D.H. Huson et al. "Dendroscope- An interactive viewer for large phylogenetic trees", BMC Bioinformatics 8:460, 2007) </text>
near the end of the file.
