Question: dxy (Nei 1987) calculation
0
gravatar for modernsynthesis
4.2 years ago by
United States
modernsynthesis30 wrote:

Is there any scripts out there that can calculate absolute divergence (dxy) between populations/species using many alignments of sequence data?

 

 

 

 

snp sequence next-gen alignment • 5.3k views
ADD COMMENTlink modified 6 weeks ago by beausoleilmo300 • written 4.2 years ago by modernsynthesis30
2

Could you give the right reference to the paper and possibly explain the terms in the equation?

ADD REPLYlink written 4.2 years ago by dariober11k
1

The equation is described in Box 1 in a recent Molecular Ecology paper by Cruickshank and Hahn (2014). Link to the open access paper: http://onlinelibrary.wiley.com/doi/10.1111/mec.12796/pdf.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by modernsynthesis30

Thanks, and I should have put this in my first comment: Do you have some example dataset to play with? (In general it's good to make life easier to those willing to answer questions...)

ADD REPLYlink written 4.2 years ago by dariober11k

Below are 3 example alignments

Locus1:

#NEXUS
begin data;
    dimensions ntax=2 nchar=460;
    format datatype=dna missing=? gap=-;
matrix
species1 ?????????????????????TAGTCCTTACACTGTAAAAAACTTTGGAATTGTTTGACCCTGTAAACACAAAATTCATGTCTCTCACCCTGGGACAAATACATTCTTTTTAAAAGCAGCATATGGGCAGCCTTGGACTGATGTTAGTTTATTGTCACTGCTTGATAACATTTAATGGAAAAGATACAAGAGTGCCAAAGAATTTTAATTATTTTTGTGATAAAGTTATATGTTCGGCCTTGAAAAAGTGGAGATAATGCTGGGATTCATTATTATTCCCAGTGTGTTTAAACAGACGACACAGAATGCAAACAAAAGCAGATGAAATTTGAAAAGTATTATCAATATT???????????????????????????????????????????????????????????????????????????????????????????????????????????????
species2 TGTGTGCATGCACAGATTTTTTAGTCCTTACACTGTAAAAAACTTTGGAATTGTTTGACCCTGTAAACACAAAATTCATGTCTCTCACCCTGGGACAAATACATTCTTTTTAAAAGCAGCATATGGGCAGCCTTGGACTGATGTTAGTTTATTGTCACTGCTTGATAACATTTAATGGAAAAGATACAAGAGTGCCAAAGAATTTTAATTATTTTTGTGATAAAGTTATATGTTCGGCCTTGAAAAAGTGGAGATAATGCTGGGATTCATTATTATTCCCAGTGTGTTTAAACAGACGACACAGAATGCAAACAAAAGCAGATGAAATTTGAAAAGTATTATCAATATTGCAGATAGCAGATGCCCTTTCCAATCAGAACAAGCATATCTTCTATAGCAACTTTATGGTTGAGTAGTTTATTCATTTCTATTAGAAGGTTGTACGTTTCTAAAATATGTA
;
end;

Locus2:

#NEXUS
begin data;
    dimensions ntax=2 nchar=582;
    format datatype=dna missing=? gap=-;
matrix
species1 ????????????????????????????????????????AACCACAATTGGTTGTCTGTTTTCTACTTTATGACATTTCCACTGAAAATTGTAATTCTTTTTTGCTGTGTTCTATTCCCCTTGTACGGAGTGTCCCCTTGGGAAGTGGGGCCCAAGAGCCCTTTCTAGGATGGGACAGGATATTACAGCTTGGTTTGTGCACCAGCATCCTTAATATTTCCTTCCTTTCAGAAGCAAATAGAGCGTACCCTTATCTGAATGCTAATTTCCTAGTTAAAACCCTCCCTTGCTGACAAGGGACTGAAAGAGTTTTAAATCACAGATGTAGAGTATCAAATGCAATAATGCTCTTGCAATAGTGCATTGAAGCCTCAATTAATTAACCCTTGGGCTAAGTAGGCAGGTACATGGTGGTGGCCACAGGCGGTGGATGGATGAGATTTAAATGGGCATCTCATTTCCTCA????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
species2 ????????????????????????????TTCTGAAAAATAAACCACAATTGGTTGTCTGTTTTCTACTTTATGACATTTCCACTGAAAATTGTAATTCTTTTTTGCTGTGTTCTATTCCCCTTGTACGGAGTGTCCCCTTGGGAAGTGGGGCCCAAGAGCCCTTTCTAGGATGGGACAGGATATTACAGCTTGGTTTGTGCACCAGCATCCTTAATATTTCCTTCCTTTCAGAAGCAAATAGAGCGTACCCTTATCTGAATGCTAATTTCCTAGTTAAAACCCTCCCTTGCTGACAAGGGACTGAAAGAGTTTTAAATCACAGATGTAGAGTATCAAATGCAATAATGCTCTTGCAATAGTGCATTGAAGCCTCAATTAATTAACCCTTGGGCTAAGTAGGCAGGTACATGGTGGTGGCCACAGGCGGTGGATGGATGAGATTTAAATGGGCATCTCATTTCCTCAGCACGGAACATGCCGTTTGATTCAGAAAGGAGTCATTTTACACACTCGCCTCATTTACGCTCAGCTTTAATCCCTTTAATTCCACCTGAGATCCAAGCAAGAATGGGAAAAGAGAG
;
end;

Locus3:

#NEXUS
begin data;
    dimensions ntax=2 nchar=610;
    format datatype=dna missing=? gap=-;
matrix
species1 ?????TATGTCTTGGTCTAGACTGAAGCAGAAACTCCAGGTCAGACATATGGTGACTGAAAAAGTGCATGTTATTTATTCATATCTCTTAATGTGAAATGTGTATTTGAAGAGACTTAAAATCTCTGAAAGAGCCAATTACTCTCAGCTTTTTAATTCTAGCAATACATTTGGAACATTTTCATTGTTCTAAGGGTTAAAAACCTCACCGTGACAATGATGAGCCTTATTACTCAGTCAAAGTAAATGGATCACCATATAACCTTTCAGAAATGTTCTTCCTTAAGCTATTAAAACATTCCATGCCCTTAGATGACAACAATTTCTCTGCCTTTTGAAATTTCTTTTCTATCCTGCAGAGTTCATAGAGATATGCTTGGTTAAAATCAACTTATATAAAACTATGCACTGTAAATTCTGACACTTCTGTTTGAATCTCTTTTCAAACACTTGTCTTTGCTCACCATAATAGATGTCAGTTCTTCTGATGTAGTTCAAGCATGAGCTTCATATGAAGACTCAGCTATGTCTATTGCATTTCTGAAGCTACTACTCACTGAAGTTTTGTGCTGTTTGACATCAAAGATAGGCAAGAATCACCTGCTGAGTTC
species2 TAAGGTATGTCTTGGTCTAGACTGAAGCAGAAACTCCAGGTCAGACATATGGTGACTGAAAAAGTGCATGTTATTTATTCATATCTCTTAATGTGAAATGTGTATTTGAAGAGACTTAAAATCTCTGAAAGAGCCAATTACTCTCAGCTTTTTAATTCTAGCAATACATTTGGAACATTTTCATTGTTCTAAGGGTTAAAAACCTCACCGTGACAATGATGAGCCTTATTACTCAGTCAAAGTAAATGGATCACCATATAACCTTTCAGAAATGTTCTTCCTTAAGCTATTAAAACATTCCATGCCCTTAGATGACAACAATTTCTCTGCCTTTTGAAATTTCTTTTCTATCCTGCAGAGTTCATAGAGATATGCTTGGTTAAAATCAACTTATATAAAACTATGCACTGTAAATTCTGACACTTCTGTTTGAATCTCTTTTCAAACACTTGTCTTTGCTCACCATAATAGATGTCAGTTCTTCTGATGTAGTTCAAGCATGAGCTTCATATGAAGACTCAGCTATGTCTATTGCATTTCTGAAGCTACTACTCACTGAAGTTTTGTGCTGTTTGACATCAAAGATAGGCAAGAATCACCTGCTGAGTTC
;
end;
ADD REPLYlink modified 3 months ago by RamRS26k • written 4.2 years ago by modernsynthesis30
2

I've implemented PI, which is very similar to dxy. https://github.com/zeeev/popFastaaa

If more people express interest I will implement dxy.

ADD REPLYlink modified 3 months ago by RamRS26k • written 4.2 years ago by Zev.Kronenberg11k
0
gravatar for polcarel
4.0 years ago by
polcarel0
polcarel0 wrote:

Hi... Back to the question above, how to calculate window-based Dxy between two populations given a set of genomewide SNP dataset using R? I am still at the early stage in R or perl.

Many thanks in advance.

ADD COMMENTlink written 4.0 years ago by polcarel0

Homework? Why use R?

ADD REPLYlink written 4.0 years ago by Adrian Pelin2.4k

I guess R would be the fastest way to do this...By the way, I eventually managed to calculate windows of 10kb nucleotide diversities (pi, π) for each population πx and πy. This may be another silly question, can I use these π values to estimate the Dxy between the two populations?

ADD REPLYlink written 4.0 years ago by polcarel0
0
gravatar for beausoleilmo
6 weeks ago by
beausoleilmo300
McGill University
beausoleilmo300 wrote:

In this paper, there is a link to their supplementary material. Within, these is a genomescan_dxy.pl.

I'm not understanding Perl enough to be able to read and interpret what is happening, but that could be one way of doing it.

ADD COMMENTlink written 6 weeks ago by beausoleilmo300
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