How can i calculate site likelihood by raxml ??

[engsam...@gmail.com]

Hi,

i am newly using raxml and i need to calculate site likelihood for one tree and i have my tree file in Newick format

but i need to know my steps and linux orders in details please .

thanks :)

[Alexandros Stamatakis]

Please have a look at the manual page 15:

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf

options: -f g and -f G

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>.
> 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
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[engsam...@gmail.com]

Thanks Alexis :)

but i have another problem during running

when i entered my order raxmlHPC -f g -s alg -m GTRGAMMA -z optimal tree file.nwk -n TEST

i found that message

 Error: please specify a name for this run with -n

i try several times to change my output file name but i found the same message.

[Mark Miller]

If there are really blank spaces in optimal tree file.nwk

I think that will cause a problem. You might try adding underscores optimal_tree_file.nwk

[engsam...@gmail.com]

Thanks alot Mark :)