I have BioCyc enzyme/pathway features that I want to represent as phylogeny, in an image. Is there any tool/database that can be used for this purpose.
What type of data do you have ? Protein sequence or nucleotide sequence ? If you have either go ahead and use clustal w or mega and make a phylogenetic tree
Thank you very much. I don't have protein sequence data, but have predicted Biocyc pathway ID's derived from microbiome OTU abundances. I can think of linking to KEGG Go ID's and use the sequences on Mega or R.
There is no way you can present this kind of data as a phylogeny. You may be able to put them into some kind of graph representation, but don't call this a phylogeny. Phylogeny is only possible if you can compare the sequences of orthologous genes. So that would only work if all components of the pathway are in the same protein family. As far as I know, no such pathway exists.
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