This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can we draw phylogenetic tree using a set of Kegg Orthology Terms ?

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

ko phylogeny kegg
• 3,704 views • link
updated by jhc jhc • written by Amk Amk

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.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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

• 0 views • link
written by Amk Amk

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

• 0 views • link
written by Michael Dondrup Michael Dondrup

Thank you Micheal.

• 0 views • link
written by Amk Amk

1 answer

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
• 0 views • link
updated by Ram Ram • written by jhc jhc

Log in to answer this question.

More posts like this