#Loading the required libraries
library(ape)
library(phangorn)
library(seqinr)
#Importing the required file
align_5 <- read.alignment("C:/Users/VAMSI/align 5.fasta", format = "fast")
align_119 <- read.alignment("C:/Users/VAMSI/align 119.fasta", format = "fasta")
Computing the distance matrix for both UPGMA and NJ algorithms implementation.
matrix_5x5 <- dist.alignment(align_5, matrix = "identity")
summary(matrix_5x5)
matrix_119x119 <- dist.alignment(align_119, matrix = "identity")
summary(matrix_119x119)
#Implementation of UPGMA algorithm for a small matrix (5x5) and entire
matrix (119x119)
UPGMA_5x5 <- upgma(matrix_5x5)
UPGMA_119x119 <- upgma(matrix_119x119)
summary(UPGMA_5x5)
summary(UPGMA_119x119)
#Implementation of NJ algorithm for a small matrix (5x5) and entire
matrix (119x119)
NJ_5x5 <- NJ(matrix_5x5)
NJ_119x119 <- NJ(matrix_119x119)
summary(NJ_5x5)
summary(NJ_119x119)
I have done this whole analysis but don't know how can I the save my
tree file in svg or some other image format . In the avove script , I
am applying the phylogenetic algorithm on the distance matrix which I
have created through fasta file
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