I am interested in one gene family, who has 16 kegg ID (K*). I extracted all the gene amino acid sequences under each one KEGG ID, but got confused about how different these amino acid sequences are. Just wondering whether you have any suggestions about how to generate phylogeny relationship across those different kegg IDs.
If you have the amino acid sequences you can just put them through the Simple Phylogeny tool (https://www.ebi.ac.uk/Tools/phylogeny/simple_phylogeny/).
Hi Robert Adolf Brinzer ,
Thanks for your advice. I forgot to mention that for kegg ID (K*), there are 1K-4K amino acid sequences. I am thinking of a way to cluster all the amino acid sequences into smaller groups first, then choose the representatives for each category in the phylogenetic tree. So would like to know how did KEGG cluster the genes into each KEGG ID category at the first place.
Cheers,
Jia
This paper may be useful for understanding how the KEGG IDs were generated (https://academic.oup.com/bioinformatics/article/21/19/3787/210373?login=true).
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