#1 merges all fasta-files in particular directory into file j.fasta
cat /P/y19/term3/block2/pr9/to_join/* > j.fasta
#2 splits file with several fasta-sequences into several files
seqretsplit /P/y19/term3/block2/pr9/to_split/coding1.fasta -auto
#4 translates nucleotide sequences to file p.fasta
transeq /P/y19/term3/block2/pr9/to_split/coding1.fasta -out p.fasta
#6 changes format from fasta to msf, applied to alignment file
seqret /P/y19/term3/block2/pr9/alignment.fasta -osformat2 msf -out alignment.msf
#10 shuffles nucleotide sequence in file 4.fasta
shuffleseq 4.fasta -auto
#11 writes 3 random sequences with length=100 into file makeseq.fasta
makenucseq -amount 3 -auto 
#15 deletes ctrl+r symbol in the end of stdin, hence translates stdin from dos format to unix and outputs to stdout
dos2unix