library(ape)
library(seqinr)
data<- read.dna('PrimateData.fasta.txt', format="fasta")
dist.dna(data, model="TN93", gamma=1)


data<- read.alignment('PrimateData.fasta.txt', format="fasta")
datamatrix<-as.matrix(data)
chisqtable <- as.matrix(array(0, dim=c(nrow(datamatrix), 4)))
row.names(chisqtable)=row.names(datamatrix)
for(j in 1:ncol(datamatrix)){
for(i in 1:nrow(datamatrix)){
if(datamatrix[i,j]=="a"){chisqtable[i,1] = chisqtable[i,1]+1}
if(datamatrix[i,j]=="c"){chisqtable[i,2] = chisqtable[i,2]+1}
if(datamatrix[i,j]=="g"){chisqtable[i,3] = chisqtable[i,3]+1}
if(datamatrix[i,j]=="t"){chisqtable[i,4] = chisqtable[i,4]+1}
}}
chisq.test(chisqtable)


data<- read.alignment('algae.fasta.txt', format="fasta")
datamatrix<-as.matrix(data)
chisqtable <- as.matrix(array(0, dim=c(nrow(datamatrix), 4)))
row.names(chisqtable)=row.names(datamatrix)
for(j in 1:ncol(datamatrix)){
for(i in 1:nrow(datamatrix)){
if(datamatrix[i,j]=="a"){chisqtable[i,1] = chisqtable[i,1]+1}
if(datamatrix[i,j]=="c"){chisqtable[i,2] = chisqtable[i,2]+1}
if(datamatrix[i,j]=="g"){chisqtable[i,3] = chisqtable[i,3]+1}
if(datamatrix[i,j]=="u"){chisqtable[i,4] = chisqtable[i,4]+1}
}}
chisq.test(chisqtable)

for(j in 2:nrow(chisqtable)){
for(i in 1:(j-1)){
print(c(i,j))
print(chisq.test(chisqtable[c(i,j),]))
}}