AA substitution matrix with parser (and ExaML)

[F]

Hi there,

Just trying ExaML for the first time.  Quick question, can I specify the substitution matrix I want to use in examl when I use parser to create my binary file? I just ran it twice and parser seems to automatically create a JTT matrix (in my case) but I would like to use WAG.  Is there a way to specify the matrix? (this is not a partitioned analysis, it's a very large supermatrix with about 500K aa sites).

Thanks!

[Alexandros Stamatakis]

Yes, what you have to do is to pass a RAxML-formatted partition file to
the parser via -q.

This partition file just needs to contain a single partition, i.e. a
single line:

WAG, p1=1-500000

where 500000 is the length of your alignment.

Alexis

--
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

[F]

Great! 

Thanks, Alexis!

[Andre J. Aberer]

Hi Felipe,

it should work. Just create a partition file using the usual RAxML
format, like that:

WAG, stretch=1-32883

and provide the partition file via -q to the parser.

HTH,
Andre

--
Best regards,
Andre Aberer

PreDoc (Bioinformatics) in the Exelixis Lab, Heidelberg Institute for Theoretical Studies

[Christian Rinke]

Hi,
When I follow these instructions I get the following error messages:

ERROR trying to assign model 0 to position 41028
while already model 0 has been assigned to this position
ERROR trying to assign model 0 to position 41123
while already model 0 has been assigned to this position
ERROR trying to assign model 0 to position 41129
while already model 0 has been assigned to this position

does this mean I have to check each alignment first manually to find the exact length?
Thanks,
Chris

[Alexey Kozlov]

Hi Chris,

yes, you do need to know the alignment length if you're using partition file.

If your alignment is in PHYLIP format then it's trivial - and you don't have to do it manually, you can write a two-line
script which will generate the partition files.

For FASTA it's a bit more tricky, but you can easily convert FASTA to PHYLIP using a script provided with RAxML
(usefulScripts/convertFasta2Phylip.sh).

Cheers,
Alexey

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[Alexandros Stamatakis]

and RAxML can also parse fasta alignment files now by the way, it will
recognize them automatically, apart from that there seems to be some
sort of error in your partition file that generates the error message
you saw,

alexis