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<p>Dear Joseph</p>
<p><br>
</p>
<p>The "left_index" and "right_index" columns are there to implement
the Nested set model (cf
<a class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Nested_set_model">https://en.wikipedia.org/wiki/Nested_set_model</a> ). They allow quick
retrieval of ancestors / descendants.</p>
<p><br>
</p>
<p>That said, if you want to export one of our speices-trees into, I
would suggest to directly download them from the FTP
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/">ftp://ftp.ensembl.org/pub/release-99/compara/species_trees/</a>, or
use the Perl script
ensembl-compara/scripts/examples/species_getSpeciesTree.pl<br>
</p>
<p><br>
</p>
<p>Best,<br>
Matthieu</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 10/04/2020 10:29, Joseph Steinberger
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:AM0P191MB0706B813C471A3D07E18260CB5DE0@AM0P191MB0706.EURP191.PROD.OUTLOOK.COM">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Dear Community -</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
How do I process a mysql <i><b>species</b></i> tree table in
order to create a newick file? </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
I would like to generally understand what 'left index' and
'right index' mean, as I think I can then process the table into
a newick file.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thank you for your time -</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Yossi</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Matthieu Muffato, Ph.D.
Ensembl Compara Principal Developer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room A3-123
Phone + 44 (0) 1223 49 4631
Fax + 44 (0) 1223 49 4468</pre>
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