How to get bootstrap output sequence as fasta format

[Aritra Mahapatra]

HI,

I need to do bootstrapping and my input sequences are in fasta format. I need to get the output in fasta format also as the rest of the parts have developed for fasta format. My question is if there is any provision to change the output file format in RAxML?

Thanking you,

[Lucas Czech]

Hi Aritra,

what exactly do want to output in fasta format? If you want to do bootstrapping, the result is a tree with bootstrap support annotations on its branches, stored in newick format. Fasta is however a format for sequences, not for trees. It thus cannot be simply converted into each other.

If I however got your question wrong and you have some other sequence or alignment format like phylip, sam, etc, and want to convert that to fasta, just look online. There are plenty of tools for that.

Best regards
Lucas

--
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.
For more options, visit https://groups.google.com/d/optout.

[Aritra Mahapatra]

Hi Lucas,

By default it gives the tree having bootstrap support. By applying -f j  option in raxml command it gives the bootstrapped sequences (the number of bootstrapped sequences should be mentioned in option -#) on which it computes the bootstrap scores. I need to use those bootstrapped sequences for my further operations.

With regards,
Aritra

[Alexandros Stamatakis]

I assume you mean the bootstrap replicate MSA files that RAxML produces
with -f j and you'd like to have these in fasta instead of phylip? correct?

Alexis

On 15.10.2017 11:47, Aritra Mahapatra wrote:
> Hi Lucas,
>

> By default it gives the tree having bootstrap support. By applying *-f
> j*  option in raxml command it gives the bootstrapped sequences (the
> number of bootstrapped sequences should be mentioned in option *-#*) on

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

>> For more options, visit https://groups.google.com/d/optout

>> <https://groups.google.com/d/optout>.

>
> --
> 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

> <mailto:raxml+un...@googlegroups.com>.

> For more options, visit https://groups.google.com/d/optout.

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Lucas Czech]

Hi Aritra,

the output of the -f j command are phylip files. I am not aware of an
option in RAxML to directly output fasta instead. There are however many
tools for converting that to fasta, google for "phylip to fasta". That
means you have to do this for every file. So, best to write a small
script for that.

Hope that helps. Let me know if you need any further help
Lucas