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Old 02-07-2012, 05:05 AM   #1
tianyub836
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Default 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!
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Old 02-07-2012, 06:32 AM   #2
zmartine
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"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.
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Old 02-07-2012, 07:26 AM   #3
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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.
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Old 02-08-2012, 02:27 AM   #4
tianyub836
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Quote:
Originally Posted by zmartine View Post
"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?
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Old 02-08-2012, 02:29 AM   #5
tianyub836
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Quote:
Originally Posted by themerlin View Post
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
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Old 02-08-2012, 03:03 AM   #6
colindaven
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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
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Old 04-19-2012, 11:09 AM   #7
Bueller_007
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Quote:
Originally Posted by zmartine View Post
"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.
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Old 09-12-2012, 02:27 PM   #8
HerefordGuy
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See http://www.pnas.org/content/early/2009/10/21/0904691106 for an example of using maximum parsimony to analyze SNP data.
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Old 01-17-2013, 10:53 AM   #9
mm.perrineau
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Hi,
No idea how construct phylogenetic tree using SNPs ???
MM
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Old 05-21-2013, 05:09 AM   #10
NGS group
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Default 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
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Old 05-21-2013, 06:27 AM   #11
Bueller_007
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Haven't used it yet, but
http://beast2.cs.auckland.ac.nz/index.php/SNAPP
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