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AxPARAFIT still in use? #1

Open Jigyasa3 opened 5 years ago

Jigyasa3 commented 5 years ago

Dear Dr Alexandros

I am trying to implement the AxPARAFIT software that you wrote for my co-evolution analysis. But even after checking the tutorial and data files, I cannot understand the following part of the code-

  1. The code is- AxParParafit[BLAS] -p numberOfPermutations -n1 N1 -n2 N2 -n3 N3 -n4 N4 -A associationMatrix -B parasiteMatrix -C hostMatrix -n runID -t traceFileName. The Test-data file contains the matrices. But how do I get to a matrix from host and symbiont ML trees?

  2. Can the program handle multiple co-evolutions i.e. some hosts are associated with multiple symbionts, while others in the phylogeny lack symbionts. eg- H1-S1, H1-S2, H1-S3, H2-0.

Looking forward to your reply. Regards Jigyasa Arora

stamatak commented 5 years ago

On 14.06.19 11:41, Jigyasa3 wrote:

Dear Dr Alexandros

I am trying to implement the AxPARAFIT software that you wrote for my co-evolution analysis. But even after checking the tutorial and data files, I cannot understand the following part of the code-

1.

The code is- AxParParafit[BLAS] -p numberOfPermutations -n1 N1 -n2
N2 -n3 N3 -n4 N4 -A associationMatrix -B parasiteMatrix -C
hostMatrix -n runID -t traceFileName.
The Test-data file contains the matrices. But how do I get to a
matrix from host and symbiont ML trees?

As far as I remember (this work was done many years ago) you have to draft the matrix yourself, that's the hypothesis you want to test.

2.

Can the program handle multiple co-evolutions i.e. some hosts are
associated with multiple symbionts, while others in the phylogeny
lack symbionts. eg- H1-S1, H1-S2, H1-S3, H2-0.

Not sure, doesn't reading the original paper:

Legendre P, Desdevises Y, Bazin E: A statistical test for host-parasite coevolution. Systematic Biology 2002,

help?

Alexis

Looking forward to your reply. Regards Jigyasa Arora

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-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org