Question: phylogenetic tree after ortholog finding by orthoMCL
0
gravatar for Mehmet
19 months ago by
Mehmet170
Japan
Mehmet170 wrote:

Dear All:

I have completed finding ortholog proteins (proteome data) of 16 species by using orthoMCL tool. After that, I want to make a phylogenetic tree based on orthologs proteins among those species. Could you please help how to do that? For instance, I have IDs of orthologs and how can I get related proteins from my own protein data (in orthoMCL output)? and use them for the phylogenetic tree?

Thank you for taking a time.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Mehmet170

Strictly speaking, you should be inferring orthologs from the phylogenetic tree, not the other way around. The procedure to build a tree is to first construct a multiple sequence alignment then use one of several methods to reconstruct the tree. This tutorial is a good introduction.
 

ADD REPLYlink written 19 months ago by Jean-Karim Heriche13k

May be he wants to build phylogeny based on conserved genes.
 

ADD REPLYlink written 19 months ago by Nari810

Possibly but by definition, orthologs can only be inferred from a tree so you can't call your sequences, however similar they are, orthologs until you've built the tree. Using pairwise alignments only is a short cut that can make mistakes. For example, between species paralogs wouldn't be detected and incorrectly called orthologs.

ADD REPLYlink written 19 months ago by Jean-Karim Heriche13k
1
gravatar for Nari
19 months ago by
Nari810
United States
Nari810 wrote:

BPGA can process OrthoMCL output to generate a 1,0 binary matrix and also processes the same to form Concatenated Orthologous core genes to construct UPGMA or NJ phylogeny on that basis. 

It's not that big proteome. so you may recluster your proteome using much faster USEARCH (included in BPGA as default). It should not take more than 5 minutes.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Nari810
0
gravatar for Mehmet
19 months ago by
Mehmet170
Japan
Mehmet170 wrote:

Hi,

After having found orthologs by orthoMCL tool, I have to isolate single copy genes from output of orthoMCL and extract these single copy genes` sequences to build a phylogenetic tree. I completed orthoMCL step, but I need help after that. How to get single copy genes and their protein sequences?

ADD COMMENTlink written 19 months ago by Mehmet170

For getting single copy genes, you have to filter your OrthoMCL output such that : The Orhologous cluster/ group (each line) contain genes (gene header/id) from all the genomes under study. but not including more than one gene from any genome. Those gene ids will help you extract protein sequences from the individual protein files by some means (maybe a small perl script). Even if you find few such clusters you can build alignment by concatenating them and generate tree based on that. The tool BPGA I mentioned is capable of doing trees on orthologous sequences but not single copy genes.

ADD REPLYlink written 18 months ago by Nari810
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 657 users visited in the last hour