Create UPGMA tree
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8 weeks ago
rjsgur789 • 0

Hello everyone. While drawing the UPGMA Tree from the VCF file, a question suddenly arises and I leave a question.

I tried to draw UPGMA Tree from SNP using R, and confirmed that it can be drawn through the following code.

library(poppr)

library(dartR)

library(vcfR)

library(radiator)

library(gdsfmt)

library(ape)

vcf <- read.vcfR("dp5q20mm90_biA.GBS177.SNP3.recode.vcf", verbose = T)

my_genind <- vcfR2genind(vcf)

aboot(my_genind, tree = "upgma", distance = "nei.dist", sample = 1000, showtree = T, missing = "mean")

However, I have confirmed that when I draw like this, the shape of the picture does not come out well, and the time loss is huge.

(177 objects, total file size 1.4G)

If you draw like this, the distance between the end line of the tree and the name of the entity will become very far, and unlike the above, it took more than an hour for just 100 repetitions.

(Desktop: Window 10, memory size = 8Gb, CPU = Intel(R) Core(TM) i5-7600 CPU @ 3.50GHZ (4 CPUs))

So, I checked in various ways, although I could find a way to indicate the branch length, I could not find a way to indicate the boot strap and check the branch.length at the same time.

Since the vcf file is very large, I want to convert it into a GDS file and draw it.

If branch.length and bootstrap can be marked at the same time, the shape of the picture is not greatly broken, it is possible to work with GDS, or if there is a way to shorten the time, I would like to get help.

Thanks in advance for your advice.

TREE SNP UPGMA R GDS • 128 views
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