pep of 10 Bacillus were downloaded from Ensembl
cat *.* >>99.00spe10_aa.txt

Bacillus_subtilis_best7613.GCA_000328745.1.19.pep.all.fa best
Bacillus_subtilis_qb928.GCA_000293765.1.19.pep.all.fa qb
Bacillus_subtilis_subsp_inaquosorum_kctc_13429.GCA_000332645.1.19.pep.all.fa ina
Bacillus_subtilis_subsp_natto_best195.GCA_000209795.1.19.pep.all.fa nat
Bacillus_subtilis_subsp_spizizenii_atcc_6633.GCA_000177595.1.19.pep.all.fa spi
Bacillus_subtilis_subsp_subtilis_str_sc_8.GCA_000230755.2.19.pep.all.fa sc

formatdb -i Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -p T

blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_best7613.GCA_000328745.1.19.pep.all.fa -o 99.01168_best.txt -m 8 -e 10
blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_qb928.GCA_000293765.1.19.pep.all.fa -o 99.01168_qb.txt -m 8 -e 10
blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_subsp_inaquosorum_kctc_13429.GCA_000332645.1.19.pep.all.fa -o 99.01168_ina.txt -m 8 -e 10
blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_subsp_natto_best195.GCA_000209795.1.19.pep.all.fa -o 99.01168_nat.txt -m 8 -e 10
blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_subsp_spizizenii_atcc_6633.GCA_000177595.1.19.pep.all.fa -o 99.01168_spi.txt -m 8 -e 10
blastall -p blastp -d Bacillus_subtilis_subsp_subtilis_str_168.GCA_000009045.1.17.pep.all.fa -i Bacillus_subtilis_subsp_subtilis_str_sc_8.GCA_000230755.2.19.pep.all.fa -o 99.01168_sc.txt -m 8 -e 10

perl 02.best_hit.pl
perl 03.alain.pl
