#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 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.