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R

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library("seqinr")

library("phangorn")

mySeqaln <- read.alignment(file ="plnR.phy", format= "phylip“)

mydist <- dist.alignment(mySeqaln)

tree.nj <- nj(mydist)

source("unrootedNJtree.r")

source("cleanAlignment.r")

cleanedrsmaln <- cleanAlignment(mySeqaln , 65, 5)

source("rootedNJtree.r")

opar <- par(mfrow = c(2, 2))

plot(tree.nj, cex.main=0.8, main = "Neighbor-Joining")

rsmtree <-unrootedNJtree(mySeqaln , type="DNA")

title("The unrooted phylogenetic tree constructed by Neighbor-Joining

method ", cex.main=0.8)

cleanedrsmtree <-unrootedNJtree(cleanedrsmaln, type="DNA")

title("The phylogenetic tree constructed by Neighbor-Joining method

after the verifying alignment", cex.main=0.8)

cleanedrsmtree <- rootedNJtree(cleanedrsmaln, "CP002222.1", type="DNA")

title("The rooted tree phylogenetic tree constructed by Neighbor-Joining

method after the verifying alignment", cex.main=0.8)

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matlab