Can we draw phylogenetic tree using a set of Kegg Orthology Terms ?

Question

[Amk]

Dear All,

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.

Thank you.
Amk

[Michael]

Like a pre-computed tree? Ensembl has something similar with the compara pipeline. compara identifies orthologs and paralogs automatically and computes a gene tree across orthologs for each gene. If you can map your KO's to Ensembl gene IDs you can view the trees in the Ensembl browser.

[Amk]

Dear Michael,

Thank you for the suggestion. It make sense. Is Compara pipeline is down now? I checked but not responding. I will try the way you said.

Thank you.
Amk

[Michael]

looks like ensembl is down at this moment, just try again later

[Michael]

it's back for me

[Amk]

Thank you Micheal.

Answer 1

[jhc]

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