treesoft-treefam — TreeFam supports and public discussions.

Re: [Treesoft-treefam] Version info

[Sebastien M. <Seb...@un...>]

> Hi,
>> Is there a simple way to get TreeFam current release ?
>>
>> Via database request or treesoft API ?
> 
> You should be able to access all Treefam versions on the MySQL server.
> We are currently working on version 6. However, the only stable version
> is the public one (currently version 4). The API goes with the public
> version. We made some modifications in Treefam 6 so the current public
> API (v4) may not work for everything.
> 
> J-K

So, if treesoft API is always up-to-date locally, we are able to know 
the current TreeFam release simply with the $Treefam::Config::APIVERSION 
or $Treefam::Config::TFDBNAME variables.

Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056

Re: [Treesoft-treefam] Version info

[Jean-Karim H. <jk...@sa...>]

Hi,
> 
> Is there a simple way to get TreeFam current release ?
> 
> Via database request or treesoft API ?

You should be able to access all Treefam versions on the MySQL server.
We are currently working on version 6. However, the only stable version
is the public one (currently version 4). The API goes with the public
version. We made some modifications in Treefam 6 so the current public
API (v4) may not work for everything.

J-K



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Treesoft-treefam] Version info

[Sebastien M. <Seb...@un...>]

Hi,

Is there a simple way to get TreeFam current release ?

Via database request or treesoft API ?

Thanks

-- 
Sébastien Moretti

[Treesoft-treefam] Erroneous map info in treefam3

[<gu...@ge...>]

Hello everyone,

I found that 5031 (31 in Arath, 5000 in Caere) genes have wrong map information.
The errors are either T_START>C_START or T_STOP<C_STOP.

Sincerely yours,
Yiran Guo

Bioinformatics Department,
Beijing Genomics Institute,
Chinese Academy of Sciences

Telephone: +86-10-80481559 (Office),
           13693087971 (Mobile, only in China)
Address: Beijing Airport Industrial Zone B-6,
         Beijing, P.R.China, Postal Code: 101300
Website: http://www.big.ac.cn/ 

 
______________ ______________ ______________ ______________
Sent via the KillerWebMail system at genomics.org.cn


 
                   

[Treesoft-treefam] Ortholog data are uploaded

[Heng Li <lh...@sa...>]

Hi,

I have uploaded ortholog/within-species paralogs to treefam ftp:
ftp://ftp.sanger.ac.uk/pub/treefam/release-3.0/flat_file/

I am sorry that I have not put this file for so long time. Jean-Karim
actually made it months ago.

regards,

Heng

[Treesoft-treefam] TreeFam live site update

[Heng Li <lh...@sa...>]

Hi all,

TreeFam home page (www.treefam.org) and download page are updated to
show the latest changes to TreeFam. TreeSoft is also introduced at the
TreeFam home page. Jean-Karim's Perl API is formally added to both of
TreeSoft and TreeFam.

What I did not say in the TreeFam home page is the openning of a public
mailing list: tre...@li.... I am not sure
whether people need a public mailing list, or whether we should put
this at SourceForge even if they need one. Alternatively, we may apply
for a Sanger one if people like. What's your opinion?

regards,

Heng