Re: Accession numbers of PhyloPhlan proteins?

[Curtis Huttenhower]

Thanks Paul, and good luck with the paper! I think the data you'll need are in the alignments files on the PhyloPhlAn page:

http://huttenhower.sph.harvard.edu/phylophlan

About ~25% of the way down the page in links labeled "400 alignments, and the subsampled concatenated alignment." If those don't have what you need, let us know?

Thanks again -

Curtis

On Tue, Sep 4, 2018 at 10:51 AM Facey P. <p.f...@swansea.ac.uk> wrote:

Dear Professor Huttenhower,

Would it be possible to point me in the direction of the list of the 400 proteins that are used in the Phylophlan pipeline? I have a manuscript almost accepted using this pipeline but a reviewer is asking for the protein accession numbers of those proteins used in the final concatenated alignment. Previously I have just cited the PhyloPhlan paper, but in this instance the reviewer is insistent that I provide a table with the information. Is there a file containing orthologous sequences for these 400 proteins (so that I can BLAST back to our isolates)?

Would be very grateful for your help.

regards

Paul

Dr. Paul D. Facey

Lecturer in Molecular Evolution

Fellow of the Higher Education Academy (FHEA)

Institute of Life Sciences 1

Swansea University Medical School

Room 528

Tel 01792 2915028