We have MAF file for alignment which need to be converted.
The MAF file was converted into .fasta format for handling with ease in the R. This step was performed in the GALAXY server by using “MAF into FASTA”. The exported file was concatenated into a single sequence which represents a single specie.
The alignment file which generated included the whole genome sequence of 54 species and small alignment file was also obtained that included only the sequences of top 5 species
R Script :
#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 do the same analysis through python
Can anyone help me plz?