#2
seqretsplit seq.fasta -auto
#4
transeq seq.fasta -frame 1 -table 0 -out protein.fasta
#5
getorf seq.fasta seq.orf -minsize 100 -auto
#10
shuffleseq seq.fasta shuffled_seq.fasta
#11
makenucseq -amount 3 -length 100 -auto
#13
tranalign seq.fasta proteinseq.fasta -auto
#14
degapseq seq.fasta degap_seq.fasta