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Robert Buels | 1 Aug 2010 21:17
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GMOD Evo Hackathon Open Call for Participation

We are seeking participants for the GMOD Tools for Evolutionary Biology 
Hackathon, held November 8-12, 2010 at the US National Evolutionary 
Synthesis Center (NESCent) in Durham, NC.

This hackathon targets three critical gaps in the capabilities of the 
GMOD toolbox that currently limit its utility for evolutionary research:

  1. Visualization of comparative genomics data
  2. Visualization of phylogenetic data and trees
  3. Support for population diversity and phenotype data

If you are interested in these areas and have relevant expertise, you 
are strongly encouraged to apply. Relevant areas of expertise include 
more than just software development: if you are a GMOD power user, 
visualization guru, domain expert (comparative, phylogenetics, 
population, ...), or documentation wizard, then your skills are needed!

How To Apply:

Fill out the online application form at http://bit.ly/gmodevohack. 
Applications are due August 25.

About GMOD:

GMOD is an intercompatible suite of open-source software components for 
storing, managing, analyzing, and visualizing genome-scale data. GMOD 
includes many widely-used software components: GBrowse and JBrowse, both 
genome viewers; GBrowse_syn, a comparative genomics viewer; Chado, a 
generic and modular database schema; CMap, a comparative map viewer; as 
well as many other components including Apollo, MAKER, BioMart,
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Mark A. Jensen | 2 Aug 2010 01:19
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Re: SOAP Eutilities

Turns out that module lives in bioperl-run; try 

git clone git://github.com/bioperl/bioperl-run.git

MAJ
----- Original Message ----- 
From: "Robson de Souza" <robfsouza <at> gmail.com>
To: <bioperl-l <at> bioperl.org>
Sent: Saturday, July 31, 2010 4:56 PM
Subject: [Bioperl-l] SOAP Eutilities

> Hi,
> 
> Bio::DB::SoapEUtilities, referred in the HOWTO on EUtilities, seems to
> have disappeared from the Git repository.
> A simple
> 
> git clone git://github.com/bioperl/bioperl-live.git
> 
> does not download it. Any ideas why?
> Robson
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>
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Dave Messina | 2 Aug 2010 15:58
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Re: phyloxml and element order

Hi Fred,

Thanks for letting us know about this — definitely sounds like a bug.

Would you please submit this to our bug tracker?

    http://bugzilla.open-bio.org

(You can just copy and paste your previous email.)

Dave

On Jul 30, 2010, at 06:59, Frédéric Romagné wrote:

> Hi,
> 
> I'm using bioperl to create phyloxml trees, after few tentatives, i got my
> tree with all the element/attributes i want but when I write the tree,
> element are not written following the order specified in the XSD Schema.
> 
> For example, i got :
> 
> <clade>
>   <clade>
>      <name>Loxosceles intermedia</name>
>      <taxonomy>
>         <scientific_name>Araneomorphae Sicariidae</scientific_name>
>      </taxonomy>
>      <sequence>
>         <accession source="Arachnoserver">969</accession>
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shalabh sharma | 2 Aug 2010 21:44
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clustalw to maf format

Hi,
    I am trying to convert clustalw to maf format.
I am trying to use AlignIO for that but its not working.

Its giving me the following error:

EXCEPTION Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::AlignIO::maf::write_aln" is not implemented by
package Bio::AlignIO::maf.
This is not your fault - author of Bio::AlignIO::maf should be blamed!

STACK Bio::Root::RootI::throw_not_implemented
/Library/Perl/5.8.8/Bio/Root/RootI.pm:707
STACK Bio::AlignIO::maf::write_aln /Library/Perl/5.8.8/Bio/AlignIO/
maf.pm:176
STACK Bio::AlignIO::PRINT /Library/Perl/5.8.8/Bio/AlignIO.pm:492
STACK toplevel msf2mafy.pl:11

Is there any other way i can convert clustalw to maf?

I would really appreciate if anyone can help me out.

Thanks
Shalabh
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Smithies, Russell | 2 Aug 2010 22:25
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Re: clustalw to maf format

This might work if you only have a few:
http://www.ibi.vu.nl/programs/convertalignwww/

--Russell

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
> bounces <at> lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Tuesday, 3 August 2010 7:45 a.m.
> To: bioperl-l
> Subject: [Bioperl-l] clustalw to maf format
> 
> Hi,
>     I am trying to convert clustalw to maf format.
> I am trying to use AlignIO for that but its not working.
> 
> Its giving me the following error:
> 
> EXCEPTION Bio::Root::NotImplemented -------------
> MSG: Abstract method "Bio::AlignIO::maf::write_aln" is not implemented by
> package Bio::AlignIO::maf.
> This is not your fault - author of Bio::AlignIO::maf should be blamed!
> 
> STACK Bio::Root::RootI::throw_not_implemented
> /Library/Perl/5.8.8/Bio/Root/RootI.pm:707
> STACK Bio::AlignIO::maf::write_aln /Library/Perl/5.8.8/Bio/AlignIO/
> maf.pm:176
> STACK Bio::AlignIO::PRINT /Library/Perl/5.8.8/Bio/AlignIO.pm:492
> STACK toplevel msf2mafy.pl:11
>
(Continue reading)

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shalabh sharma | 2 Aug 2010 22:53
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Re: clustalw to maf format

Hi Russell,
            Thanks for the reply, but i  have around 400 alignments and some
huge ones :(

Thanks
Shalabh

On Mon, Aug 2, 2010 at 4:25 PM, Smithies, Russell <
Russell.Smithies <at> agresearch.co.nz> wrote:

> This might work if you only have a few:
> http://www.ibi.vu.nl/programs/convertalignwww/
>
> --Russell
>
>
> > -----Original Message-----
> > From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
> > bounces <at> lists.open-bio.org] On Behalf Of shalabh sharma
> > Sent: Tuesday, 3 August 2010 7:45 a.m.
> > To: bioperl-l
> > Subject: [Bioperl-l] clustalw to maf format
> >
> > Hi,
> >     I am trying to convert clustalw to maf format.
> > I am trying to use AlignIO for that but its not working.
> >
> > Its giving me the following error:
> >
> > EXCEPTION Bio::Root::NotImplemented -------------
(Continue reading)

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Peter | 2 Aug 2010 23:24
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Re: clustalw to maf format

On Mon, Aug 2, 2010 at 8:44 PM, shalabh sharma
<shalabh.sharma7 <at> gmail.com> wrote:
> Hi,
>    I am trying to convert clustalw to maf format.
> I am trying to use AlignIO for that but its not working.

Could you tell us why you have to use maf format?
I'm curious because all of the phylogenetics tools I've
had to work with personally will take some other format
which is more widely supported (e.g. FASTA, PFAM,
ClustalW, PHYLIP, ...).

Peter
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Bernd Web | 2 Aug 2010 23:25
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Re: clustalw to maf format

Hi Shalabh,

This ConvertAlign does not write maf either, it only reads it (i made
it). I found some other converters on the web but they do not export
to maf format either...

http://biotechvana.uv.es/servers/afc/main.php
http://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

Galaxy has a MAF to Fasta converter:
http://main.g2.bx.psu.edu/root?tool_id=MAF_To_Fasta1

Regards,
Bernd

On Mon, Aug 2, 2010 at 10:53 PM, shalabh sharma
<shalabh.sharma7 <at> gmail.com> wrote:
> Hi Russell,
>            Thanks for the reply, but i  have around 400 alignments and some
> huge ones :(
>
> Thanks
> Shalabh
>
>
> On Mon, Aug 2, 2010 at 4:25 PM, Smithies, Russell <
> Russell.Smithies <at> agresearch.co.nz> wrote:
>
>> This might work if you only have a few:
>> http://www.ibi.vu.nl/programs/convertalignwww/
(Continue reading)

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Chris Fields | 2 Aug 2010 23:31
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Re: clustalw to maf format

No other format will work?  The main reason you see unimplemented methods like this is there is no active
interest in working with this format beyond getting the information stored within them into objects and
other commonly-used formats.

chris

On Aug 2, 2010, at 3:53 PM, shalabh sharma wrote:

> Hi Russell,
>            Thanks for the reply, but i  have around 400 alignments and some
> huge ones :(
> 
> Thanks
> Shalabh
> 
> 
> On Mon, Aug 2, 2010 at 4:25 PM, Smithies, Russell <
> Russell.Smithies <at> agresearch.co.nz> wrote:
> 
>> This might work if you only have a few:
>> http://www.ibi.vu.nl/programs/convertalignwww/
>> 
>> --Russell
>> 
>> 
>>> -----Original Message-----
>>> From: bioperl-l-bounces <at> lists.open-bio.org [mailto:bioperl-l-
>>> bounces <at> lists.open-bio.org] On Behalf Of shalabh sharma
>>> Sent: Tuesday, 3 August 2010 7:45 a.m.
>>> To: bioperl-l
(Continue reading)

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shalabh sharma | 3 Aug 2010 00:30
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Re: clustalw to maf format

Hi All,
      Thanks for the replies.
Actually i am working on a pipeline involving RNAz.
I had impression that there must be a converter available as their webserver
can take xmfa or maf format but standalone is only accepting maf format.

I think i will use a program that can output as xmfa and write to those
people if they can provide me with the converter.

Thanks
Shalabh

On Mon, Aug 2, 2010 at 5:31 PM, Chris Fields <cjfields <at> illinois.edu> wrote:

> No other format will work?  The main reason you see unimplemented methods
> like this is there is no active interest in working with this format beyond
> getting the information stored within them into objects and other
> commonly-used formats.
>
> chris
>
> On Aug 2, 2010, at 3:53 PM, shalabh sharma wrote:
>
> > Hi Russell,
> >            Thanks for the reply, but i  have around 400 alignments and
> some
> > huge ones :(
> >
> > Thanks
> > Shalabh
(Continue reading)

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Gmane