Question: Can we draw phylogenetic tree using a set of Kegg Orthology Terms ?
0
gravatar for Amk
3.4 years ago by
Amk120
Amk120 wrote:

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

kegg phylogeny ko • 1.3k views
ADD COMMENTlink modified 3.4 years ago by jhc2.8k • written 3.4 years ago by Amk120
1

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.

ADD REPLYlink written 3.4 years ago by Michael Dondrup46k

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

ADD REPLYlink written 3.4 years ago by Amk120

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

ADD REPLYlink written 3.4 years ago by Michael Dondrup46k
1

it's back for me

ADD REPLYlink written 3.4 years ago by Michael Dondrup46k

Thank you Micheal.

ADD REPLYlink written 3.4 years ago by Amk120
1
gravatar for jhc
3.4 years ago by
jhc2.8k
Germany
jhc2.8k wrote:

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 

```

ADD COMMENTlink written 3.4 years ago by jhc2.8k
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