tag:treefam.tenderapp.com,2013-02-16:/discussionsTreeFam: Recent Discussions 2024-03-20T00:16:40Ztag:treefam.tenderapp.com,2013-02-16:Discussion/208485922022-03-10T15:33:57Z2022-03-10T15:34:05ZEBI Search indexing<div><p>Good afternoon team,</p>
<p>I am Ossama Edbali, part of the EBI Search team at The European Bioinformatics Institute.<br>
In regards to TreeFam, we index data from a specific location in EBI's noah cluster.<br>
We're currently migrating to a new cluster (codon) and we found that the numbers of entries stated in the XML data feed (TreeFam9.xml) is 15,737 although the actual number of entries is 15,736.</p>
<p>This was working because there were no updates since 2013 (hence indexing was not happening), but whilst re-running indexing in a new cluster we uncovered this issue. Is it possible to fix this mismatch? Thank you.</p>
<p>Our points of contact are Mateus Patricio and/or Matthieu Muffato, and we wanted to check if they are still valid points of contact.</p>
<p>Best regards,<br>
Ossama Edbali</p></div>Ossama Edbalitag:treefam.tenderapp.com,2013-02-16:Discussion/194076982020-10-12T20:44:12Z2020-10-15T14:59:20Zre: color of the nodes<div><p>Dear Pasha,</p>
<p>There are two symbols for internal nodes:<br>
- duplications are shown as red triangles, - speciations are show as green circles. Leaves are always black squares.</p>
<p>Hope this helps,<br>
Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/189547742019-07-11T08:44:22Z2019-07-12T08:40:45ZFailed to connect to TreeFam MySQL server<div><p>Hi, Matthieu<br>
Thank you very much!<br>
It is working well now.</p></div>Syunwuntag:treefam.tenderapp.com,2013-02-16:Discussion/179521472018-01-30T12:49:34Z2018-01-31T18:37:17ZAmphimedon accessions<div><p>Hi Emily</p>
<p>Treefam is in the middle of a reorganization of the phylogenetic analyses of Ensembl and Ensembl Genomes. We have generated a new library of HMMs that are going to be used across all Ensembl sites later this year (see <a href="http://www.ensembl.org/info/genome/compara/hmm_lib.html">http://www.ensembl.org/info/genome/compara/hmm_lib.html</a> and <a href="ftp://ftp.ensembl.org/pub/current_compara/">ftp://ftp.ensembl.org/pub/current_compara/</a> )<br>
At the moment we don't know how the treefam.org website is going to change.</p>
<p>Kind regards,<br>
Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/151109922015-06-02T15:40:36Z2020-06-16T16:08:31ZIssues with some of the TFs and perl API get_families.pl script<div><p>With the Perl API, one can fetch a tree for TF314013 that contains all the subfamilies.<br>
As this stands, the subfamilies are just the product of our own limitation when computing the alignment, trees, etc, and displaying them. The only family that ought to be used is TF314013.</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/169148842017-03-23T23:04:06Z2020-06-16T16:08:31ZTreefam error<div><p>Hi Krikita,</p>
<p>It would be useful if you could share a minimal data file that causes<br>
the error, together with the command-line you used.<br>
I would like to check what is happening under the hood, and whether<br>
there is a case that is not handled by the script</p>
<p>Thank you,<br>
Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/160968592016-06-02T11:24:42Z2018-10-19T08:27:58ZTreeFam-A Download<div><p>Thank you very much for your help Matthieu. I'll try to fetch
the data from the MySQL server.</p></div>Bas Verbruggentag:treefam.tenderapp.com,2013-02-16:Discussion/160212012016-05-03T08:57:14Z2016-05-04T17:30:58ZRegarding the output file.<div><p>Dear Gauri,</p>
<p>The output in your screenshot already tells you the homologies.
Indeed we don't have (yet) a standalone tool to infer the trees and
the orthologies.<br>
If you want to build orthologies for a whole proteome, you'd
currently have to get the existing alignments + trees of all the
families and run tools yourselves. We'd recommend Mafft + RAxML +
some custom parsing of the trees. Unfortunately all our pipelines
require an infrastructure that is still difficult to setup and is
not much tested outside of our own environment, so I think its cost
would outweigh the burden of running things on your own</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/155877372015-11-04T14:08:27Z2016-08-11T03:27:33ZAwaiting annotation link is broken<div><p>Steps to reproduce</p>
<ol>
<li>Go to the Gene Tree tab <a href="http://www.treefam.org/family/TF333215#tabview=tab1">http://www.treefam.org/family/TF333215#tabview=tab1</a></li>
<li>Click the link in "TreeFam gene tree for family awaiting
annotation."</li>
<li>
<p>This returns this url:</p>
<p><a href="http://www.treefam.org/family/awaiting%20annotation">http://www.treefam.org/family/awaiting%20annotation</a></p>
</li>
</ol>
<p>Which gives this error message:</p>
<pre>
<code>There was a problem loading the requested page. Invalid TreeFam accession number specified
You might like to go back to the previous page, search for the entry you’re looking for. If you think that there is a problem with the server, please report it via the email address at the bottom of the page. Please be sure to include the URL for the page that you were trying to view.</code>
</pre>
<p>Best,<br>
Matt</p></div>tag:treefam.tenderapp.com,2013-02-16:Discussion/155877262015-11-04T14:04:58Z2015-11-04T14:04:59Ztree type / branch length settings interaction problem<div><p>Steps to reproduce</p>
<ol>
<li>Go to the Gene Tree tab <a href="http://www.treefam.org/family/TF333215#tabview=tab1">http://www.treefam.org/family/TF333215#tabview=tab1</a></li>
<li>Under the Control elements section -> branch length, click
"Real"</li>
<li>Under the Control elements section -> Tree type, click
"Full"</li>
<li>The branch length is reset to cladogram in the actual tree but
the branch length radio button erroneously remains "Real".</li>
<li>Under the Control elements section -> branch, click
"Cladogram". This makes the actual branch length in the tree
"Real", reversed from how it should be.</li>
</ol>
<p>Best,<br>
Matt</p></div>tag:treefam.tenderapp.com,2013-02-16:Discussion/155876922015-11-04T13:52:48Z2015-11-04T13:52:49ZNaN in "How to cite annotation"<div><p>On the tree for MC4R</p>
<pre>
<code>http://www.treefam.org/family/TF332646#tabview=tab1</code>
</pre>
<p>Clicking on the how to cite link in the Gene Tree section, the
description has a "NaN" rather than the TreeFam family name:</p>
<pre>
<code>The TreeFam family NaN (NaN,TF332646) has 189 from 57 species.</code>
</pre>
<p>Perhaps, if the tree doesn't have a name the description should
not put in NaN. Also there appears to be a missing noun (sequence,
gene, protein?), as well, so it could instead read</p>
<pre>
<code>The TreeFam family TF332646 has 189 MISSING_NOUN from 57 species.</code>
</pre>
<p>Overall this is a great service, thanks!</p>
<p>Best,<br>
Matt</p></div>tag:treefam.tenderapp.com,2013-02-16:Discussion/153958122015-08-31T19:43:42Z2018-10-19T08:27:58ZAbout the NHX format<div><p>Dear Matthieu,</p>
<p>Thank you very much for the useful information! :-) I will do as
you suggested to remove the "TCOGS2:" string from all the
files.</p>
<p>Best wishes,<br>
Fang-Yu</p></div>Fang-Yu Raotag:treefam.tenderapp.com,2013-02-16:Discussion/151552502015-06-16T15:36:11Z2020-06-16T16:08:31ZClone MySQL database<div><p>Dear Patrick</p>
<p>Yes you can clone the database with mysqldump -utreefam_ro
-hmysql-treefam-public.ebi.ac.uk -P4418 --skip-lock-tables
treefam_production_9_69</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/148045492015-02-24T16:09:01Z2015-06-09T15:35:46ZTreeFam.hmm <div><p>Hi Nick,</p>
<p>Sorry for the long reply, but we were not receiving
notifications from the forum (this is now fixed !).<br>
Thank you for your email, we have now updated the documentation
accordingly</p>
<p>Regards,<br>
Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/150580582015-05-20T10:47:55Z2018-10-19T08:27:58ZAdding gene to phylogeny<div><p>Very useful yes. THanks for your help.</p>
<hr>
<p>From: mateus <a href="mailto:tender2+d8305ccd15@tenderapp.com">tender2+d8305ccd15@tenderapp.com</a><br>
Sent: Tuesday, June 09, 2015 9:26 AM<br>
To: McGrath, Patrick T<br>
Subject: TreeFam support: Adding gene to phylogeny [Questions]</p>
<p>?</p></div>McGrath, Patrick Ttag:treefam.tenderapp.com,2013-02-16:Discussion/150575122015-05-20T09:13:11Z2015-06-08T16:02:41ZSome TreeFam MySQL Tables Empty<div><p>Dear Aine,</p>
<p>Yes, it is expected that many tables are empty. The database has
the same schema as Ensembl Compara, which defines tables to store
whole-genome alignments, and many other types of analyses</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Discussion/144779682014-10-31T14:40:43Z2015-06-08T14:42:16ZTF102023 in download page files<div><p>Dear treefam support,</p>
<p>I noticed that a certain treefam family (TF102023) was not
present in the downloadable files 'treefam9.fa.tar.gz' and
'treefam_family_data.tar.gz'. On the</p>
<p>Could you explain to me why some families are missing and what I
should do to get the full set of ortholog data?</p></div>tag:treefam.tenderapp.com,2013-02-16:Discussion/139303582014-06-12T11:27:24Z2015-06-08T14:41:31ZTreeFam Conversion Tables<div><p>I am trying to find a translation table between UCSC IDs, RefSeq
and TreeFam IDs for mouse (specifically mm10) and human
(specifically hg19).</p>
<p>If this is not possible, is there a conversion table between
TreeFamID and gene symbol? I see that the download page has a
hgnc_treefam.txt link (<a href=
"http://www.treefam.org/static/download/hgnc_treefam_txt">http://www.treefam.org/static/download/hgnc_treefam_txt</a>),
but unfortunately it is broken. Does similar information also exist
for mouse?</p>
<p>Thanks.</p></div>tag:treefam.tenderapp.com,2013-02-16:Discussion/136373332014-04-11T23:12:49Z2015-06-08T14:06:37Zconsensus sequence<div><p>Thanks Fabian for your replies,<br>
It seems like we cannot download your HMM, since when you click on
them you get 'Page Not Found' error like :<br>
<a href=
"http://www.treefam.org/family/TF101007/hmm">http://www.treefam.org/family/TF101007/hmm</a></p>
<p>And it's not also available in your bulk download pages
either</p></div>Fayetag:treefam.tenderapp.com,2013-02-16:Discussion/136373302014-04-11T23:11:40Z2014-04-14T07:51:00Zcds sequences<div><p>Dear Faye,<br>
thanks for your question.<br>
We get all our CDS sequences from ensembl. Both protein and CDS are
used in the tree building process. We use TreeBest to build a CDS
alignment. It uses the protein alignment as a guide.</p>
<p>Does that help?</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/136373142014-04-11T23:05:49Z2014-04-14T07:48:16Zpfam vs treefam<div><p>Hi Faye,<br>
thanks for your interest in TreeFam.<br>
Pfam and TreeFam are different databases. While TreeFam tries to
find all gene families of full length protein sequences, Pfam tries
to identify conserved regions (e.g. domains, motifs) within those
full length protein sequences.<br>
The fact that Pfam has many larger families tells us that domains
seem to be more widely conserved than full length protein
sequence.<br>
Does that make sense?</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/123157892013-09-20T18:15:30Z2015-06-08T13:54:22ZHow to get proteomes used in treefam9?<div><p>closed for now</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/127613562013-11-17T16:18:39Z2015-06-08T14:02:58ZTreeFam treefam_scan.pl gene families<div><p>Hi Diana.</p>
<p>You should be able to download that information from the
download section (families with annotations):<br>
<a href=
"http://www.treefam.org/static/download/treefam9_family_annotation.tab.tar">
http://www.treefam.org/static/download/treefam9_family_annotation.t...</a></p>
<p>Please let us know of any other queries.<br>
Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Discussion/123154952013-09-20T17:30:18Z2015-06-08T13:54:21Ztreefam db mysql access<div><p>Hi miafond,<br>
thanks for pointing that out.<br>
We have changed the mysql command on the website.</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/121166522013-08-21T00:13:12Z2013-08-24T23:45:16ZRaw data access<div><p>Dear jnotwell,<br>
thanks for your message.<br>
We have a public MySQL server. It is available using the following
command:</p>
<p>mysql -hmysql-treefam-public.ebi.ac.uk -P4418 -u treefam_ro</p>
<p>Hope that helps!</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/120831362013-08-14T14:39:47Z2015-06-08T14:00:19ZCannot see the gene tree on the web<div><p>Hi Akihiko.</p>
<p>Could you please give it a try on another browser, like: Firefox
or Chrome.</p>
<p>Because unfortunately right now we don't support IE. And I
assume that is the problem.</p>
<p>Please let me know if that doesn't work either, then we can
investigate it more thoroughly.</p>
<p>Do not hesitate in contacting us for any further query.</p>
<p>Cheers,</p>
<p>Mateus.</p></div>mateustag:treefam.tenderapp.com,2013-02-16:Discussion/118470472013-07-01T13:49:46Z2015-06-08T13:54:21ZGENE TREES: Downloading the full view<div><p>Hi Amit,<br>
thanks for your reply.</p>
<p>We have found a way to provide zooming for our gene trees. We
currently test it, but it should make its way into the next
release.</p>
<p>Also, I am optimistic that we find a solution to download the
gene trees.<br>
There are some interesting approaches available.<br>
Thanks for your help!</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/119137842013-07-14T15:51:12Z2015-06-08T13:54:22ZNumber of Proteins in TreeFam<div><p>Dear Andy,<br>
thanks for your message and sorry for the late reply.<br>
You are right, the number of orphan genes is quite high.</p>
<p>The answer is that some of those genes should be in a family<br>
but are currently not.<br>
We are looking into ways of building many new families in an
automated way.</p>
<p>But once again, currently this number is high and we expect to
reduce it soon.</p>
<p>Hope that answers your question.</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/118213712013-06-26T07:50:14Z2013-06-26T08:22:31ZManual curation in TreeFam 9<div><p>Dear Michael,<br>
thanks for your message.<br>
You are right, the TreeFam database was built - similar to Pfam and
Rfam -<br>
with the idea of having an A- and a B-section. (You are also right
that there is currently no documentation about this, which we will
add shortly)<br>
Up to release 4 or 5, TreeFam put a lot of effort into manually
curating TreeFam A families, or curating TreeFam-B families that
would then move into TreeFam-B.</p>
<p>As you might know, TreeFam uses TreeBest to build reconciled
gene trees for every family. At some point it was tested whether
the trees build from TreeBest are as good as the ones that were
manually curated. Turned out, they are equally good.<br>
That was reason enough to not curate families anymore.<br>
Bear in mind that there are three problems with the manual curation
of families:<br>
1. It is very time-consuming<br>
2. depends on subjective choices made by the curator (difficult to
come up with clear set of rules)<br>
3. the gene tree topology can change dramatically depending on the
input alignment.</p>
<p>I hope that helps. If not, please don't hesitate to ask for more
details.</p>
<p>Cheers,<br>
Fabian</p></div>Fabiantag:treefam.tenderapp.com,2013-02-16:Discussion/116278112013-05-21T09:32:26Z2013-06-14T08:56:00ZCONSERVATION OF GENES- INCLUDING FUNGI AND PLANTS<div><p>Hi Jim,<br>
thanks for your feedback.</p>
<p>You are right, there are differences between TreeFam, Ensembl
Compara and HomoloGene, which are due to the different methodology
or taxon sampling.<br>
Also, we keep our families fixed TreeFam and whereas e.g. Compara
rebuild their families with every release. There are good arguments
for either approach.</p>
<p>At some time in the near future we will be looking into ways of
testing our families. We will then also cross-check our predictions
with e.g. Ensembl. That is a good idea.</p>
<p>Thanks again for your valuable feedback!<br>
I will close the ticket for now, as we have added your suggestions
to our todo list for the evaluation of our families</p>
<p>Cheers,<br>
Fabian</p></div>Fabian