mask columns using site-weights

[Anton Savchenko]

Hi all,

A question on --site-weights option: if I want to exclude partitions/sites from analysis, but do not want to actually cut the alignment, is it possible to work around by making a column weight file with zeroes for excluded columns and ones for included columns?

Thanks!

Best,

Anton

[Alexandros Stamatakis]

Hi Anton.

I believe this should work, or you might get an error message that the
weight is zero.

Personally though, I'd still remove these sites from the MSA prior te
analyzing it, if I had to do this analysis.

Alexis

> --
> 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>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/feb8ac53-eaa9-4952-8a3b-12652755b89cn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/feb8ac53-eaa9-4952-8a3b-12652755b89cn%40googlegroups.com?utm_medium=email&utm_source=footer>.

--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)

[Anton Savchenko]

Thanks, Alexandros.

Indeed, it doesn't work with null weights: "ERROR: Non-positive site weight found: 0".

Anton