Converting a NEXUS file to a PHYLIP file

[qspreng...@gmail.com]

Hello,

I am trying to run RAxML for the first time. I have a single NEXUS file that contains alignments for 35 taxa scored for 1750 loci (two alleles each). I am having trouble converting this to a PHYLIP file. Any suggestions? 

Thanks,

Quentin

[Almir Pepato]

Dear Quentin,

I've never had problems using Mesquite for exporting Nexus as Phylip. Which program are you using for handling your data?

Cheers, 

2013/9/14 <qspreng...@gmail.com>

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Prof. Almir Rogério Pepato
UFMG/ICB/Depto. Zoologia
Laboratório de Sistemática e Evolução de Ácaros Acariformes
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[qspreng...@gmail.com]

Hi Dr. Pepato,

Thanks for the suggestion, Mesquite did the trick. When I then run a rapid bootstrap it looks at the single alignment for each species instead of the alignments for 1750 loci independently. Do you how to parse the data so RAxML will look at the alignments for each locus?

[Almir Pepato]

Hi! 

For partitioning your data in RAxML you must provide as input a text file containing the concatenated alignment partition ranges and call for it using the option -q. The partition input has a syntax like: DNA,p1 = 1-582 DNA, p2 = 583-1064...

As you have a large number of loci, I strongly recommend employing a Perl script or something alike. If you are not used to it, you can employ the FASconCAT, kindly provided at: http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/FASconCAT/index.en.html

The output of FASconCat includes the ranges you need for RAxML in a .xml file.

all the best!

2013/9/15 <qspreng...@gmail.com>

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[Alexandros Stamatakis]

there's also a RaxML option "-f s" that splits up a concatenated
alignment into per-partition alignments if you provide a RAxML partition
file via -q,

alexis

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[qspreng...@gmail.com]

Thanks Alexis,

It split my concatenated file into 1750 gene/partition alignment files. How do I now run a rapid bootstrap  with using each of all of these alignments?

Thanks again,

Quentin

[Alexandros Stamatakis]

you will need to send me your input files such that I can help you, are
you using the latest RAxML version from github?

Alexis

On 09/16/2013 04:25 PM, qspreng...@gmail.com wrote:
> Thanks Alexis,
>
> My command line looks like this: ./raxmlHPC -f s -q Gavia_35tx_1750loci.phy
> -s Loon_Data5.phy -m GTRCAT -n TEST2
> Where Gavia_35tx_1750loci.phy is my partition file and Loon_Data5.phy is
> the concatenated alignment. It will not run but instead says Segmentation
> fault: 11. What am I doing wrong?
>
> Thanks so much,
> Quentin

>
> On Saturday, September 14, 2013 4:57:41 PM UTC-4, qspreng...@gmail.com
> wrote:
>

[Alexandros Stamatakis]

you will have to write a little script that invokes the rapid BS algo on
each per-partition alignment,

alexis

>>> 2013/9/15 <qspreng...@gmail.com <javascript:>>

>>>
>>>> Hi Dr. Pepato,
>>>>
>>>> Thanks for the suggestion, Mesquite did the trick. When I then run a
>> rapid
>>>> bootstrap it looks at the single alignment for each species instead of
>> the
>>>> alignments for 1750 loci independently. Do you how to parse the data so
>>>> RAxML will look at the alignments for each locus?
>>>>
>>>>
>>>> On Saturday, September 14, 2013 4:57:41 PM UTC-4,
>> qspreng...@gmail.comwrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to run RAxML for the first time. I have a single NEXUS
>> file
>>>>> that contains alignments for 35 taxa scored for 1750 loci (two alleles
>>>>> each). I am having trouble converting this to a PHYLIP file. Any
>>>>> suggestions?
>>>>>
>>>>> Thanks,
>>>>> Quentin
>>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>> Groups
>>>> "raxml" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>> an

>>>> email to raxml+un...@googlegroups.com <javascript:>.