On 12/3/20 7:12 PM, Anas Jamshed wrote:
#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
SVG format is for graphics. I don't see any R graphics calls or anything
I recognize as a "tree". (Perhaps the summary function for objects
returned from `upgma` include graphics? I surely do not know.)
Cairo graphics is supported in the grDevices package. It should be
loaded by default. Have your tried this at your console:
?svg
--
David.
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