I have done pathway annotation report with Kegg Orthology IDs for my species of interest. Can I draw a phylogeny tree, using some of the KO IDs(more than ten) or genes from the report. I thought of fetch gene names and put it in uniprot and extract fasta file and do a multiple sequence alignment. But I would like to know whether we have any tools to draw the tree using KO IDs only.
If you can suggest me any other way, kindly share.
If you have all your sequences in a single fasta file, you could use the same approach as in the eggNOG database (similar data) to build a phylogenetic tree. I recently added this and other workflows to the ETE toolkit, so you only need a single command line to reproduce it:
ete3 build -a fasta_file.fa -o my_tree/ -w eggnog41