Question: Phylogenetic Tree construction
1
gravatar for ammarsabir15
2.3 years ago by
ammarsabir1560
ammarsabir1560 wrote:

I have predicted Y-DNA haplogroup for individual samples using the offline version of Vadim Urasin’s YPredictor (http://predictor.ydna.ru/). Now I want to make a phylogenetic tree like the one that is shown here http://imgur.com/a/UULsu . I have data in following format(first few lines)

Haplogroup  DYS393  DYS390  DYS19   DYS391  DYS385a DYS385b DYS388  DYS439  DYS389I DYS392  DYS389II    DYS458  DYS437  DYS448  DYS449  DYS460  Y_GATA_H4   DYS456  DYS576  DYS570  DYS438  DYS481  DYS635  DYS533  DYS643  
j1    12    23  14  10  14  16  16  9   13  11  29  18  11  22  30  10  12  15  16  16  15     22   22  12  10  
I2a (xI2a1) 19  24  15  10  13  14  13  11  13  11  29  17  12  21  28  9   11  17    17    19  14  28  21  12  10
R1a 13  25  17  11  17  14  12  11  13  11  31  40  12  20  33  12  13  15  17  19    14    23  23  12  10  
I2a (xI2a1) 19  24  15  10  12  14  13  11  13  11  29  17  12  23  28  9   13  17   17 18  14  28  21  12  11
R1b 12  24  14  18  19  14  12  12  13  13  29  16  12  19  27  11  13  17  18  17  15  22  23  11  11  
  I2a   (xI2a1) 13  24  15  10  12  14  13  11  13  11  29  17  12  24  28  9   11  17  17  18  14  28  21  12  10

I have tried this using ape but ape just draws a tree based on a given dataset. Is there any package that draws the tree after comparing the results of given samples with Y-DNA haplgroup tree?

y-dna phylogenetics R • 931 views
ADD COMMENTlink modified 2.2 years ago by grant.hovhannisyan1.8k • written 2.3 years ago by ammarsabir1560

How would you define the distance between two entries, and what is represented by your data? The link to the predictor won't work.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Michael Dondrup46k
0
gravatar for grant.hovhannisyan
2.2 years ago by
grant.hovhannisyan1.8k wrote:

That looks like a RM-MJ network, is it? If yes, then try http://www.fluxus-engineering.com/Network4600_user_guide.pdf software. I am not sure that RM or MJ algorithms are implemented in R. Alternatively you can calculate genetic distances using Arlequin and construct distance based tree, using MEGA lets say.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by grant.hovhannisyan1.8k
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