blastall -i my_proteins.txt -d /flower/db/nr -p blastp -o results.br -I T;
blast2blast results.br -ecut e-50 -save -delete;
shatterblast results_mod.br -word 2;
rm results_mod.br;
blast2gi *.br -save;
gi2genbank *.gi -timeout 50 -tries 0 -append;
feature2fasta *.gb -defline '$gi|$organism|$definition' -save;
fauniq *.fa -basis sequence -save;
foreach_file *_uniq.fa -command='clustalw -infile={} -align -type=protein';
foreach_file *.aln -command='clustalw -infile={} -tree -kimura -tossgaps';