Convert vcf file to genind and the distance matrix

(Pairwise distances between individuals present in the genind object)

1. Convert VCF to genind object

load package poppr

2. Generate a UPGMA tree

We obtain an asymmetric distance matrix

genlight_Muricea <- vcfR2genlight(Muricea_filtered_no_clone_DP_Miss90_MAF_vcf_last)
library(poppr)

Muricea_tree_FINAL <- aboot(genlight_Muricea, tree = "upgma", distance = bitwise.dist, sample = 100, showtree = T, cutoff = 50, quiet = T)

genind_Muricea <- vcfR2genind(Muricea_filtered_no_clone_DP_Miss90_MAF_vcf_last)
genind_Muricea
Muricea_distances_FINAL.dist<-diss.dist(genind_Muricea, mat=TRUE, percent = TRUE)

Write distance dataframe as a table

Convert this dataframe to be able to read in another programs

Excel

write.table(Muricea_distances_FINAL.dist, file="Muricea_distances_FINAL.dist.txt", col.names = TRUE, row.names = TRUE, quote = FALSE)

write.csv(Muricea_distances_FINAL.dist, file="Muricea_distances.dist_FINAL.csv", col.names = TRUE, row.names = TRUE, quote = FALSE)