parameter is switched off meaning sequences were not saved in

y format

ect::readFASTA('SARS.HIV.fasta',bin=FALSE)

code shown below was used for the pair-wise homology

ts between 17 sequences to generate homology scores,

matrix(0,length(x),length(x))

core)=1

in 1:(length(x)-1))

in (i+1):length(x))

e[i,j]=pairwiseAlignment(x[i],x[j],

pe='local',substitutionMatrix=S,

pOpening=-1.3,gapExtension=-0.3)@score

wards, a score matrix was generated, for which a heatmap was

. The heatmap is shown in Figure 7.10. It can be seen that six

uences were closely clustered together while ten SARS-CoV-2

s were closely clustered together. However, one SARS-CoV and

equences had a smaller difference.

ignment-free approach was also applied to compare these 17

s. The function countPattern of Biostrings was used to

3-mer word frequency for these 17 sequences using the following

trix(0,length(x),length(word))

in 1:length(x))

j in 1:length(word))

r[i,j]=countPattern(word[j],x[i])

i,]=mer[i,]/sum(mer[i,])

es(mer)=c(rep('S',10),'X',rep('H',6))

comp(mer)