<div dir="ltr"><div><div><div><div><div><div>Hi Matthieu,<br><br></div>thank you for your suggestion, it fixed the problem.<br><br></div>However, I still get the following error:<br><br>mysql> SELECT * FROM msg;<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------+----------+<br>| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------+----------+<br>| 9 | copy_ncbi_table | 1 | 5 | 3 | 3 | 2018-01-15 14:49:29 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |<br>| 9 | copy_ncbi_table | 2 | 6 | 4 | 4 | 2018-01-15 14:50:36 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |<br>| 10 | populate_method_links_from_db | 3 | 7 | 6 | 6 | 2018-01-15 14:52:06 | 0 | WRITE_OUTPUT | Successfully copied 19 'method_link' rows | 0 |<br>| 16 | create_mlss_ss | 4 | 10 | 9 | 9 | 2018-01-15 14:55:10 | 0 | WRITE_OUTPUT | The species-set could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 5 | 10 | 10 | 10 | 2018-01-15 14:56:11 | 1 | WRITE_OUTPUT | The species-set could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 6 | 10 | 11 | 11 | 2018-01-15 14:57:12 | 2 | WRITE_OUTPUT | The species-set could not be found in the master database | 1 |<br>| 16 | create_mlss_ss | 7 | 10 | 12 | 12 | 2018-01-15 14:58:21 | 3 | WRITE_OUTPUT | The species-set could not be found in the master database | 1 |<br>+-------------+-------------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+------------------------------------------------------------+----------+<br>7 rows in set (0.01 sec)<br><br></div>But my species_set in the master_db is not empty:<br><br>mysql> SELECT * FROM species_set;<br>+----------------+--------------+<br>| species_set_id | genome_db_id |<br>+----------------+--------------+<br>| 1 | 1 |<br>| 1 | 2 |<br>| 2 | 1 |<br>| 2 | 3 |<br>| 3 | 1 |<br>| 3 | 4 |<br>| 4 | 1 |<br>| 4 | 5 |<br>| 5 | 2 |<br>| 5 | 3 |<br>| 6 | 2 |<br>| 6 | 4 |<br>| 7 | 2 |<br>| 7 | 5 |<br>| 8 | 3 |<br>| 8 | 4 |<br>| 9 | 3 |<br>| 9 | 5 |<br>| 10 | 4 |<br>| 10 | 5 |<br>| 11 | 1 |<br>| 12 | 2 |<br>| 13 | 3 |<br>| 14 | 4 |<br>| 15 | 5 |<br>| 16 | 1 |<br>| 16 | 2 |<br>| 16 | 3 |<br>| 16 | 4 |<br>| 16 | 5 |<br>+----------------+--------------+<br>30 rows in set (0.00 sec)<br><br></div>I am quite puzzled by this error.<br><br></div>Cheers,<br></div>Francesco.<br></div><div class="gmail_extra"><br><div class="gmail_quote">2018-01-12 17:48 GMT+01:00 Matthieu Muffato <span dir="ltr"><<a href="mailto:muffato@ebi.ac.uk" target="_blank">muffato@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Francesco<br>
<br>
Homoeologues are only used when running on plant genomes (which have polyploid genomes), but the pipeline configuration is shared and expects this method_link to be present<br>
<br>
This how it looks in the Ensembl Plants database. You can insert this row in your database and it should work<br>
<br>
<a href="http://ensro@mysql-eg-publicsql.ebi.ac.uk:4157/ensembl_compara_plants_38_91" rel="noreferrer" target="_blank">ensro@mysql-eg-publicsql.ebi.a<wbr>c.uk:4157/ensembl_compara_plan<wbr>ts_38_91</a> [Fri Jan 12 16:46:32 2018] > SELECT * FROM method_link WHERE method_link_id = 206;<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
| method_link_id | type | class |<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
| 206 | ENSEMBL_HOMOEOLOGUES | Homology.homology |<br>
+----------------+------------<wbr>----------+-------------------<wbr>+<br>
<br>
Regards,<br>
Matthieu<span class=""><br>
<br>
On 12/01/18 14:01, Francesco Lamanna wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
Hi Mateus,<br>
<br>
I could solve this problem by commenting out the line: "die "The master dabase must be defined with a collection" if $self->o('master_db') and not $self->o('collection');"<br>
<br>
in LoadMembers_conf.pm. The member_db is now correctly set up.<br>
<br>
However, when I run the Protein trees pipeline I get the following error message<br>
<br>
mysql> SELECT * FROM msg;<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
| analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
| 9 | copy_ncbi_table | 1 | 5 | 3 | 3 | 2018-01-12 14:21:39 | 0 | WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node' rows | 0 |<br>
| 9 | copy_ncbi_table | 2 | 6 | 4 | 4 | 2018-01-12 14:25:27 | 0 | WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name' rows | 0 |<br>
| 10 | populate_method_links_from_db | 3 | 7 | 6 | 6 | 2018-01-12 14:26:54 | 0 | WRITE_OUTPUT | Successfully copied 18 'method_link' rows | 0 |<br>
| 16 | create_mlss_ss | 4 | 10 | 9 | 9 | 2018-01-12 14:29:56 | 0 | FETCH_INPUT | Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm line 70. | 1 |<br>
| 16 | create_mlss_ss | 5 | 10 | 10 | 10 | 2018-01-12 14:30:57 | 1 | FETCH_INPUT | Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm line 70. | 1 |<br>
| 16 | create_mlss_ss | 6 | 10 | 11 | 11 | 2018-01-12 14:31:58 | 2 | FETCH_INPUT | Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm line 70. | 1 |<br>
| 16 | create_mlss_ss | 7 | 10 | 12 | 12 | 2018-01-12 14:33:00 | 3 | FETCH_INPUT | Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm line 70. | 1 |<br>
| 16 | create_mlss_ss | 8 | 10 | 13 | 13 | 2018-01-12 14:38:36 | 1 | FETCH_INPUT | Cannot find the method_link 'ENSEMBL_HOMOEOLOGUES' at /home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/Pre<wbr>pareSpeciesSetsMLSS.pm line 70. | 1 |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-----------------+----------+<br>
8 rows in set (0.01 sec)<br>
<br>
I wasn't aware about this method_link.<br>
<br>
Do you know how can I fix this?<br>
<br>
Thanks,<br>
Francesco.<br>
<br></span>
2018-01-11 13:28 GMT+01:00 Francesco Lamanna <<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a> <mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>>:<span class=""><br>
<br>
Hi Mateus,<br>
<br>
if I try to initialize the LoadMemebers pipeline without<br>
“--collection ensembl”, I get the following error:<br>
<br>
The following options are missing:<br>
{'collection'}<br>
<br>
I also tried to set 'collection' => undef, in the conf file, but I<br>
get another error:<br>
<br>
The master dabase must be defined with a collection at<br>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/PipeConfig/<wbr>LoadMembers_conf.pm<br>
line 190.<br>
<br>
Cheers,<br>
Francesco<br>
<br>
2018-01-11 12:01 GMT+01:00 Mateus Patricio <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br></span>
<mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<span class=""><br>
<br>
Hi Francesco,<br>
<br>
In your case the solution should be starting the LoadMembers<br>
without the option “--collection ensembl”.<br>
<br>
If you start the pipeline without it, it should use all the<br>
current species in your master database.<br>
<br>
In Ensembl we have different collections that are used for<br>
different purposes, and the default one is “ensembl”.<br>
<br>
Please let me know if this works.<br>
<br>
Cheers,<br>
<br>
Mateus.<br>
<br>
<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
On 11 Jan 2018, at 10:13, Francesco Lamanna<br>
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br></span><div><div class="h5">
<mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>> wrote:<br>
<br>
Hi Mateus,<br>
<br>
many thanks for your answer.<br>
<br>
I am trying to launch the LoadMembers pipeline in order to<br>
make a member_db, but I get the following error:<br>
<br>
mysql> SELECT * from msg;<br>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
| analysis_id | logic_name | log_message_id |<br>
job_id | role_id | worker_id | when_logged | retry |<br>
status | msg | is_error |<br>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
| 3 | copy_table_from_master | 1 | 4 | 3 | 3 | 2018-01-11 11:04:02 | 0 |<br>
WRITE_OUTPUT | Successfully copied 1646504 'ncbi_taxa_node'<br>
rows | 0 |<br>
| 3 | copy_table_from_master | 2 | 5 | 4 | 4 | 2018-01-11 11:05:46 | 0 |<br>
WRITE_OUTPUT | Successfully copied 2504391 'ncbi_taxa_name'<br>
rows | 0 |<br>
| 4 | load_genomedb_factory | 3 | 3 | 5 | 5 | 2018-01-11 11:07:06 | 0 |<br>
FETCH_INPUT | Could not fetch collection ss with name=ensembl<br>
at<br>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 4 | 3 | 6 | 6 | 2018-01-11 11:08:00 | 1 |<br>
FETCH_INPUT | Could not fetch collection ss with name=ensembl<br>
at<br>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 5 | 3 | 7 | 7 | 2018-01-11 11:08:25 | 2 |<br>
FETCH_INPUT | Could not fetch collection ss with name=ensembl<br>
at<br>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
line 106. | 1 |<br>
| 4 | load_genomedb_factory | 6 | 3 | 8 | 8 | 2018-01-11 11:09:25 | 3 |<br>
FETCH_INPUT | Could not fetch collection ss with name=ensembl<br>
at<br>
/home/hd/hd_hd/hd_cc141/EnsEMB<wbr>L/ensembl-compara/modules/Bio/<wbr>EnsEMBL/Compara/RunnableDB/<wbr>GenomeDBFactory.pm<br>
line 106. | 1 |<br>
+-------------+---------------<wbr>---------+----------------+---<wbr>-----+---------+-----------+--<wbr>-------------------+-------+--<wbr>------------+-----------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>-+----------+<br>
6<br>
<br>
Cheers,<br>
Francesco.<br>
<br>
2018-01-10 17:31 GMT+01:00 Mateus Patricio <<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a><br></div></div>
<mailto:<a href="mailto:mateus@ebi.ac.uk" target="_blank">mateus@ebi.ac.uk</a>>>:<span class=""><br>
<br>
Hi Francesco<br>
<br>
The protein tree pipeline reuses the genes and sequence<br>
members from the 'reuse_db' parameter, which in this case<br>
should point to a members database.<br>
<br>
This members database can be created by running the<br>
LoadMembers pipeline.<br>
<br>
You can initiate the pipeline with the following command line:<br>
<br></span>
<a href="http://init_pipeline.pl" rel="noreferrer" target="_blank">init_pipeline.pl</a> <<a href="http://init_pipeline.pl/" rel="noreferrer" target="_blank">http://init_pipeline.pl/</a>><span class=""><br>
Bio::EnsEMBL::Compara::PipeCon<wbr>fig::EBI::Ensembl::LoadMembers<wbr>_conf<br>
--collection ensembl<br>
<br>
Then you should point the parameter reuse_db to this<br>
database on your Protein Tree config file.<br>
<br>
'reuse_db' => 'mysql://ensro@host:port/datab<wbr>ase',<br>
<br>
Please do let me know if you have further questions.<br>
<br>
Cheers,<br>
<br>
Mateus.<br>
<br>
<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
On 10 Jan 2018, at 16:06, Francesco Lamanna<br>
<<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmail.com</a><br></span><div><div class="h5">
<mailto:<a href="mailto:francesco.lamanna@gmail.com" target="_blank">francesco.lamanna@gmai<wbr>l.com</a>>> wrote:<br>
<br>
Hi all,<br>
<br>
when I try to run the protein tree pipeline (v91) using<br>
the core Human and Chicken genomes I get the following<br>
error message:<br>
<br>
mysql> SELECT * from msg;<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
| analysis_id | logic_name |<br>
log_message_id | job_id | role_id | worker_id |<br>
when_logged | retry | status | msg<br>
| is_error |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
| 9 | copy_ncbi_table | 1 | 5 | 3 | 4 |<br>
2018-01-10 16:40:13 | 0 | WRITE_OUTPUT | Successfully<br>
copied 1646504 'ncbi_taxa_node' rows | 0 |<br>
| 9 | copy_ncbi_table | 2 | 6 | 4 | 3 |<br>
2018-01-10 16:42:04 | 0 | WRITE_OUTPUT | Successfully<br>
copied 2504391 'ncbi_taxa_name' rows | 0 |<br>
| 10 | populate_method_links_from_db<br>
| 3 | 7 | 6 | 6 |<br>
2018-01-10 16:43:44 | 0 | WRITE_OUTPUT | Successfully<br>
copied 18 'method_link' rows | 0 |<br>
| 25 | genome_member_copy | 4 | 13 | 11 | 11 |<br>
2018-01-10 16:47:49 | 0 | FETCH_INPUT | ParamError:<br>
value for param_required('reuse_db') is required and has<br>
to be defined | 1 |<br>
| 25 | genome_member_copy | 5 | 14 | 12 | 12 |<br>
2018-01-10 16:47:49 | 0 | FETCH_INPUT | ParamError:<br>
value for param_required('reuse_db') is required and has<br>
to be defined | 1 |<br>
+-------------+---------------<wbr>----------------+-------------<wbr>---+--------+---------+-------<wbr>----+---------------------+---<wbr>----+--------------+----------<wbr>------------------------------<wbr>------------------------------<wbr>--------------+----------+<br>
<br>
I have no clue about what to put in the 'reuse_db'<br>
parameter (nor could I find any information in the<br>
compara docs).<br>
<br>
Can anyone please help me to solve this issue?<br>
<br>
Thanks,<br>
Francesco.<br>
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</span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
-- <br>
Matthieu Muffato, Ph.D.<br>
Ensembl Compara and TreeFam Project Leader<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus, Hinxton<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br>
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