BEAUti command line

[Francesco Cicconardi]

Dear all,

I'd like to run a *BEAST analysis using several loci. Using the graphical interface of BEAUti would be very very time consuming and not very reproducible. Is there a batch way to create the xml file?

thanks

F

[Axel Barlow]

We ran into a similar problem when we needed to run the same analysis but with many different sets of individuals. So we generated a starting xml in beauti with the first taxon set,  then generated a perl script to automatically replace the relevant taxon elements and sequences within the xml with new ones. Then we could generate a whole bunch of different xml files in an automated fashion. These were run in beast from the command line.

There may be different/better approaches, but this is the what we came up with. I'd be really interested to hear how other people have tackled this.

Regards, Axel.

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Dr. Axel Barlow

Institute for Biochemistry and Biology
University of Potsdam
Karl-Liebknecht-Str. 24-25
14476 Potsdam (Golm)
Germany

email: axel.ba...@gmail.com
phone: +49 3319776327

[Francesco Cicconardi]

Hi Axel,

I was thinking at the same approach, but in my case I don't have to replace xml section, rather building a brand new xml file more or less from scratch... Is there anything easier?

Best

F

[Andrew Rambaut]

There is a tool called BEASTgen which you can use to create templates and then apply multiple datasets to them using a command line:

https://code.google.com/p/beast-mcmc/downloads/detail?name=BEASTGen_v1.0.tgz

It is very general purpose so you can use it to create BEAST, MrBayes or other files. There are some example templates in the package and some

brief instructions. 

Andrew

[Batsi]

hi, thank you for the BEASTgen application. I have a fasta alignment with sequence names in the following format: accession_location_subtype_year

I have pasted first block on my xml code below. I first ran without the "${taxon.location}" and I got my xml, but it did not assign the dates correctly. I then added the "${taxon.location}" and I got an error that it is null or missing. I wanted to ask how I can format in the template to retrieve the location and year correctly.

<!-- The list of taxa to be analysed (can also include dates/ages).          -->
<!-- ntax=${taxon_count}                                                                 -->
<taxa id="taxa">
  <#list taxa as taxon>
  <taxon id="${taxon.id}">
    <date value="${taxon.date}" direction="forwards" units="years"/>
    <attr name="location">
      "${taxon.location}"
    </attr>
  </taxon>
  </#list>
</taxa>

On Monday, 11 August 2014 12:44:12 UTC-4, rambaut wrote:

There is a tool called BEASTgen which you can use to create templates and then apply multiple datasets to them using a command line:

https://code.google.com/p/beast-mcmc/downloads/detail?name=BEASTGen_v1.0.tgz

It is very general purpose so you can use it to create BEAST, MrBayes or other files. There are some example templates in the package and some

brief instructions. 

Andrew

On 11 Aug 2014, at 17:35, Francesco Cicconardi <fran...@gmail.com> wrote:

Hi Axel,

I was thinking at the same approach, but in my case I don't have to replace xml section, rather building a brand new xml file more or less from scratch... Is there anything easier?

Best

F

2014-08-11 16:46 GMT+02:00 Axel Barlow <axel.b...@gmail.com>:

We ran into a similar problem when we needed to run the same analysis but with many different sets of individuals. So we generated a starting xml in beauti with the first taxon set,  then generated a perl script to automatically replace the relevant taxon elements and sequences within the xml with new ones. Then we could generate a whole bunch of different xml files in an automated fashion. These were run in beast from the command line.

There may be different/better approaches, but this is the what we came up with. I'd be really interested to hear how other people have tackled this.

Regards, Axel.

On 11.08.2014 15:29, Francesco Cicconardi wrote:

Dear all,

I'd like to run a *BEAST analysis using several loci. Using the graphical interface of BEAUti would be very very time consuming and not very reproducible. Is there a batch way to create the xml file?

thanks

F

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Dr. Axel Barlow

Institute for Biochemistry and Biology
University of Potsdam
Karl-Liebknecht-Str. 24-25
14476 Potsdam (Golm)
Germany

email: axel.b...@gmail.com
phone: +49 3319776327

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[Batsi]

So I managed to get the dates right using:

beastgen.jar -date_order -4 -date_prefix _ beastTemplate.template seqs_final.fas seqs_final.xml

The only thing left is assigning the location.

Regards,

Batsi