[EMBOSS] EMBASSY/PHYLIP Question: which option do I use to bootstrap with FPROTPARS

[Peter Rice]

Dear Michael,

On 05/03/10 14:26, michael watson (IAH-C) wrote:
> Hello
> 
> Perhaps I am missing something fundamental, but I'd like to draw a phylogenetic tree of some protein sequences I have, and use bootstrapping for confidence.
> 
> The phylip help pages seem to suggest I can do this by setting the resampling option to "bootstrap" but I cannot find this option in FPROTPARS.
> 
> I'm using EMBOSS-6.1.0 and PHYLIPNEW-3.68

My understanding of the phylip documentation is that you use (EMBOSS
name) fseqboot to generate the bootstrap resampling of your original
sequences and then use fprotpars to analyse the resulting output.

In the original phylip package the seqboot application bootstraps
several types of data. In the EMBASSY package, to make the input types
clearer, we split it into fseqboot, fseqbootall, fdiscboot, ffreqboot
and frestboot.

Hope that helps,

Peter Rice