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Phylogenetic Profile Matrix

Hi all,

How can I get a gene phylogenetic profile matrix which contains present/absent information of genes in a handful of species?

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updated by Asaf Asaf • written by ewre ewre

1 answer

You can download one from STRING database.
Choose Download on top and download the file species.mappings.v9.1.txt.gz you can pretty easily generate a matrix from this file.

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written by Asaf Asaf

Hi Asaf, I have downloaded the file you mentioned above, It has 3 columns, but I cann't figure out how to generate the matrix. can you provide some clues to do this?

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written by ewre ewre

The first column is taxonomy ID, the second is group of proteins and the third the number of representatives of the group in the genome. You can convert it pretty easily to a matrix form by putting True in the matrix where the TXID and the protein family appear in a row and False otherwise. You should need to program a bit.

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written by Asaf Asaf

I got the idea. what does the third column exactly mean in this table?

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written by ewre ewre

Number of representatives of the COG group in the genome

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written by Asaf Asaf

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