Pairwise distance matrix from RAxML?

[Mariana Meneguzzi]

Dear Alexandros, 

I have a basic question: Does the program provide a pairwise nucleotide distance matrix? 

My goal is to use the matrix to perform an ordination plot. 

I may have overlooked this information - apologies if so.

 Thank you for your time!

Mariana 

[Grimm]

Hi Mariana,

classic RAxML8 can export a ML-model based and optimised distance matrix using the MSA and a guide tree but it comes in a non-standard list format:

taxon1 taxon2 distance

taxon1 taxon3 distance

taxon1 taxon4 distance

...

which you have to parse yourself into a distance matrix.

Command is  -f x, the tree can be read in with -t, e.g.

raxmlHPC -s Matrix.epf -m GTRGAMMA -f x -t RAxML_bestTree    — without partitioning scheme

raxmlHPC -s Matrix.epf -m GTRGAMMA -f x -t RAxML_bestTree -q partition_file    — using a partitioning scheme

/G.

[Alexandros Stamatakis]

exactly :-) thanks Guido,

Alexis

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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)

[Mariana Meneguzzi]

Thank you, Guido and Alexis, for getting back to me! :)

Just to clarify, I was asking if the RAXML can output a genome pairwise distance matrix along with the tree. 
I do not have the Matrix.epf to feed in the command. 

Thank you very much!

Mariana 

[Grimm]

"Matrix.epf" is just a placeholder name for the MSA. You of course have to read in your matrix and tree.

/G