RAxML-EPA help

[Martha]

Hi everyone,

I'm new to using RAxML-EPA, and I'm pretty lost as to what I'm doing. I'm trying to place Illumina HiSeq reads on a tree built through CIPRES gateway. My libraries contain 5-7M reads, and when I try to run RAxML-EPA it finishes in ~1s and the tree doesn't really make sense.

My command is: ./raxmlHPC-SSE3 -f y -s A_23S.phy -t RAxML_bestTree.result -m GTRCAT -n A_23S --epa-keep-placements=1 --epa-prob-threshold=1

Here's a portion of the tree I get back: ((QUERY___42249_2,JN558012:0.00000050000025001454):0.00000050000025001454,(QUERY___42249_2,JN558008:0.00000050000025001454):0.00000050000025001454,(QUERY___42249_2,((QUERY___42249_2,JN558009:0.00000050000025001454):0.00000050000025001454,(QUERY___42249_2,((QUERY___42249_2,JN558010:0.00000050000025001454):0.00000050000025001454,

I know this is a very, very basic question. Thanks for any help you can provide.

[Alexandros Stamatakis]

dear martha,

that all looks fine, however you are conducting the placement with
parsimony and not likelihood (-f y option) for likelihood based
placement you would use -f v

for the output formats and supprt check the jplace file that can
conveniently be visualized using http://itol.embl.de/

hope this helps,

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

[Martha]

Hi Alexis,

Thank you, that fixed the issue. I appreciate the help!

Martha

[Alexandros Stamatakis]

:-)

alexis