how to construct phylogenetic tree using SNPs

tianyub836 · 02-07-2012, 06:05 AM

hi,
i am puzzled of how to construct phylogenetic tree using SNPs from re-sequence data.

may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes?

any details will be appreciated!

zmartine · 02-07-2012, 07:32 AM

"may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes?"

That's exactly what you can do. It's not really even an artificial sequence, since the SNPs, by definition, are the informative sites that a phylogeny is based upon, i.e. all the other sequence would be is filler that is filtered out of by the programs.

The only issue with just using the SNPs outside of a genomic context is that you will not know where they are in the codons and thus cannot use amino acid sequences for any analyse,s or know if a SNP represents a synonymous change (amino acid remains the same) or non-synonymous (changes amino acid sequence). Knowing if there is an amino acid change can be important for functional/medical genomics, for more complex codon-based models use to build phylogenies, and for selecting neutral (non-synonymous) changes to look at analyses using the molecular clock.

themerlin · 02-07-2012, 08:26 AM

I found this link the other day that constructs a phylogeny from SNPs in kmers:

http://www.omicsonline.org/2157-7145...7145-1-107.php

You have to ask the author for the source code, but it appears to work with both assemblies and raw sequence reads.

tianyub836 · 02-08-2012, 03:27 AM

Quote:

Originally Posted by zmartine

"may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes?"

That's exactly what you can do. It's not really even an artificial sequence, since the SNPs, by definition, are the informative sites that a phylogeny is based upon, i.e. all the other sequence would be is filler that is filtered out of by the programs.

The only issue with just using the SNPs outside of a genomic context is that you will not know where they are in the codons and thus cannot use amino acid sequences for any analyse,s or know if a SNP represents a synonymous change (amino acid remains the same) or non-synonymous (changes amino acid sequence). Knowing if there is an amino acid change can be important for functional/medical genomics, for more complex codon-based models use to build phylogenies, and for selecting neutral (non-synonymous) changes to look at analyses using the molecular clock.

well, thanks.
but will you give more details about constructing tree like how the SNPs and its position in chromosome are orgnized?

tianyub836 · 02-08-2012, 03:29 AM

Quote:

Originally Posted by themerlin

I found this link the other day that constructs a phylogeny from SNPs in kmers:

http://www.omicsonline.org/2157-7145...7145-1-107.php

You have to ask the author for the source code, but it appears to work with both assemblies and raw sequence reads.

that is out of my understanding

colindaven · 02-08-2012, 04:03 AM

Would it make sense to generate n artificial sequences with the SNPs and their codon contexts for
all strains of interest ?

Alternatively, I guess SNPs can be used as characters in a parsimony based approach ? Has anyone
tried this ?

Lastly, this program may also be helpful.

http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Bueller_007 · 04-19-2012, 12:09 PM

Quote:

Originally Posted by zmartine

"may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes?"

That's exactly what you can do. It's not really even an artificial sequence, since the SNPs, by definition, are the informative sites that a phylogeny is based upon, i.e. all the other sequence would be is filler that is filtered out of by the programs.

That's only true for maximum parsimony. Maximum likelihood and Bayesian methods consider invariant sites.

HerefordGuy · 09-12-2012, 03:27 PM

See http://www.pnas.org/content/early/2009/10/21/0904691106 for an example of using maximum parsimony to analyze SNP data.

mm.perrineau · 01-17-2013, 11:53 AM

Hi,
No idea how construct phylogenetic tree using SNPs ???
MM

NGS group · 05-21-2013, 06:09 AM

Dear all,

I will really appreciate if anyone would share their workflow for creating the phylogenetic tree by SNPs? Is there any commercial software that can do it?

Thank you very much!

Victor

Bueller_007 · 05-21-2013, 07:27 AM

Haven't used it yet, but
http://beast2.cs.auckland.ac.nz/index.php/SNAPP

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02-07-2012, 06:05 AM	#1
tianyub836 Member Location: China Join Date: Apr 2011 Posts: 23	how to construct phylogenetic tree using SNPs hi, i am puzzled of how to construct phylogenetic tree using SNPs from re-sequence data. may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes? any details will be appreciated!

05-21-2013, 06:09 AM	#10
NGS group Member Location: Netherlands Join Date: Apr 2013 Posts: 28	The workflow for creating phylogenetic tree by SNPs Dear all, I will really appreciate if anyone would share their workflow for creating the phylogenetic tree by SNPs? Is there any commercial software that can do it? Thank you very much! Victor

02-07-2012, 07:32 AM	#2
zmartine Junior Member Location: NIH, NIAID (USA) Join Date: Nov 2009 Posts: 4	"may i extract validated SNPs of all to generate a artificial sequence and import it to MEGA or other programes?" That's exactly what you can do. It's not really even an artificial sequence, since the SNPs, by definition, are the informative sites that a phylogeny is based upon, i.e. all the other sequence would be is filler that is filtered out of by the programs. The only issue with just using the SNPs outside of a genomic context is that you will not know where they are in the codons and thus cannot use amino acid sequences for any analyse,s or know if a SNP represents a synonymous change (amino acid remains the same) or non-synonymous (changes amino acid sequence). Knowing if there is an amino acid change can be important for functional/medical genomics, for more complex codon-based models use to build phylogenies, and for selecting neutral (non-synonymous) changes to look at analyses using the molecular clock.

02-07-2012, 08:26 AM	#3
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	I found this link the other day that constructs a phylogeny from SNPs in kmers: http://www.omicsonline.org/2157-7145...7145-1-107.php You have to ask the author for the source code, but it appears to work with both assemblies and raw sequence reads.

02-08-2012, 04:03 AM	#6
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Would it make sense to generate n artificial sequences with the SNPs and their codon contexts for all strains of interest ? Alternatively, I guess SNPs can be used as characters in a parsimony based approach ? Has anyone tried this ? Lastly, this program may also be helpful. http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

09-12-2012, 03:27 PM	#8
HerefordGuy Junior Member Location: Missouri Join Date: Apr 2010 Posts: 6	See http://www.pnas.org/content/early/2009/10/21/0904691106 for an example of using maximum parsimony to analyze SNP data.

01-17-2013, 11:53 AM	#9
mm.perrineau Member Location: New Jersey Join Date: Sep 2012 Posts: 12	Hi, No idea how construct phylogenetic tree using SNPs ??? MM

05-21-2013, 07:27 AM	#11
Bueller_007 Member Location: Earth Join Date: May 2010 Posts: 16	Haven't used it yet, but http://beast2.cs.auckland.ac.nz/index.php/SNAPP