Question: SNP matrix to a nice phylogenetic tree
2
gravatar for roy.granit
17 months ago by
roy.granit810
Israel/LabWorm
roy.granit810 wrote:

Hi All,

I have matrix with SNP calling for several positions in 6 bacterial genomes relative to a ref. sample. (generated using snippy)

For example:

gene       position   wt   sample_1     sample_2 ...
nm_1234    123        A      C              T
nm_1234    129        G      T              A

Now my goal is to find the distance between the different species and display it on a nice plot like this :enter image description here

Any suggestions on hoe to approach this? Thanks!

snp phylogenetics R • 950 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by roy.granit810
1

Past threads that may be useful:

ADD REPLYlink written 17 months ago by genomax76k

Thanks. I was able to use FastTree to convert the data into Newick format, now I need to find a way to plot it was nicely as in the figure.. would be happy to receive suggestions

ADD REPLYlink modified 17 months ago • written 17 months ago by roy.granit810

After creating Newick file ,I used Dendroscope to create the "radial" plot

ADD REPLYlink written 17 months ago by roy.granit810
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