diff --git a/Examples/commands/5-Align.sh b/Examples/commands/5-Align.sh
index 81eb407d93173093bef0ff5f489cac0d336e564b..00e43f813ad6659621d93c0251f093fd7877f671 100644
--- a/Examples/commands/5-Align.sh
+++ b/Examples/commands/5-Align.sh
@@ -1 +1,5 @@
+# run example (after running annotate, pan and core steps)
 PanACoTA align -c Examples/4-corepers/PersGenome_<pangenome-filename>_1.lst -l Examples/2-res-prokka/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/2-res-prokka -o Examples/5-align
+
+# only run align step of example
+PanACoTA align -c Examples/input_files/align-input/coregenome-example.lst -l Examples/input_files/pan-input/LSTINFO-list_genomes.lst -n GENO3_1 -d Examples/input_files/pan-input -o Examples/5-align
\ No newline at end of file
diff --git a/Examples/input_files/align-input/coregenome-example.lst b/Examples/input_files/align-input/coregenome-example.lst
new file mode 100644
index 0000000000000000000000000000000000000000..cf2b22cbc020f59b8fd7b577b2f90b62a80a0230
--- /dev/null
+++ b/Examples/input_files/align-input/coregenome-example.lst
@@ -0,0 +1,6 @@
+3 GEN4.1111.00001.0001i_00005 GENO.0321.00001.0002i_00005 GENO.1216.00002.0001i_00006
+4 GEN4.1111.00001.0001i_00008 GENO.0321.00001.0002i_00010 GENO.1216.00002.0002b_00009
+5 GEN4.1111.00001.0001b_00009 GENO.0321.00001.0002b_00011 GENO.1216.00002.0002b_00010
+7 GEN4.1111.00001.0001i_00002 GENO.0321.00001.0002b_00003 GENO.1216.00002.0001i_00003
+9 GEN4.1111.00001.0001i_00007 GENO.0321.00001.0002i_00009 GENO.1216.00002.0001b_00008
+11 GEN4.1111.00001.0001i_00004 GENO.0321.00001.0002i_00004 GENO.1216.00002.0001i_00005
diff --git a/Examples/input_files/pan-input/Genes/GEN4.1111.00001.gen b/Examples/input_files/pan-input/Genes/GEN4.1111.00001.gen
new file mode 100644
index 0000000000000000000000000000000000000000..d5c426371e32800c11fc2fb1013a41642a4b0e09
--- /dev/null
+++ b/Examples/input_files/pan-input/Genes/GEN4.1111.00001.gen
@@ -0,0 +1,128 @@
+>GEN4.1111.00001.0001b_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
+AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
+TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
+GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
+TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
+GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
+GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
+CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
+CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
+TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
+GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
+TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAGCAGCGG
+GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
+GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
+>GEN4.1111.00001.0001i_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
+CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
+CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTATGCG
+TTTGTGCATATGACGCTGAAAATCGGTACCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTC
+GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
+CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
+GTACACGCGTTATTTAAATAG
+>GEN4.1111.00001.0001i_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
+ATGCTCGATAAACAGACCCATACCCTGATCGCCCAGCGACTTAATCAGGCTGAAAAACAG
+CGTGAACAAATTCGCGCAGTGTCGCTGGATTATCCCAACATCACTATTGAAGATGCCTAT
+GCCGTACAGCGTGAATGGGTCAATATCAAGATCGCCGAAGGGCGCACGCTCAAAGGCCAC
+AAAATCGGCCTGACCTCAAAAGCGATGCAGGCCAGCTCGCAAATCAGCGAACCGGATTAC
+GGCGCGCTGCTTGACGATATGTTCTTCCATGACGGCGGCGATATCCCCACCGACCGTTTT
+ATCGTCCCGCGTATTGAAGTGGAGCTGGCGTTCGTGCTGGCGAAACCGCTGCGCGGCCCT
+CACTGCACGCTGTTCGACGTCTACAACGCCACGGATTATGTGATTCCGGCGCTGGAACTG
+ATTGACGCCCGCAGCCACAACATCGACCCGGAAACCCAGCGCCCGCGCAAAGTGTTCGAC
+ACCATTTCCGACAACGCCGCCAACGCCGGGGTGATCCTCGGTGGTCGCCCCATCAAACCA
+GACGAGCTGGATCTGCGCTGGATCTCCGCGCTGCTCTATCGCAACGGCGTGATCGAAGAA
+ACCGGCGTCGCCGCAGGCGTGCTGAATCATCCGGCCAACGGCGTGGCGTGGCTGGCGAAC
+AAGCTTGCCCCCTACGATGTCCAGCTTGAAGCCGGGCAGATCATCCTCGGCGGCTCGTTC
+ACCCGCCCGGTGCCGGCGAGCAAGGGCGACACCTTCCATGTCGATTACGGCAACATGGGC
+GCGATCAGTTGCCGGTTTGTGTAA
+>GEN4.1111.00001.0001i_00004 1404 NA | hypothetical protein | NA | NA | NA
+ATGCCCGTGAATAAGTTCTCCCGACGTACCCTCCTGACGGCAGGTTCCGCGCTTGCTGTT
+CTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
+AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
+ACCGTGGTCTTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
+GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
+TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
+GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGACGATGAGCGGCTTTGGCCCCGTC
+GCGCAAATTTTCATCGGCGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
+ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
+GGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTGCAGGGGGACGCCATTGAGTGGAAT
+GTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
+ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
+AGTTATCCTGAAGATCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
+TGCCGACAGCTGGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
+AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCCATT
+TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCTGGGATGCTC
+ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
+GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
+GGCAACATCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
+CTGCATAATCAACCGCAGCACCTCTTTCTGCGTAATATCAACGTGATGCAAACTTCAGCG
+ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
+GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
+AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
+TCGCTGCCGAAGCGGGGAGGGTAA
+>GEN4.1111.00001.0001i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
+CTGAAAGGGGTATCGTTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
+GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
+GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
+GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
+TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
+CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
+ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
+GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
+TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
+GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCCCGCCATGTCTCTTCG
+CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
+GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
+>GEN4.1111.00001.0001i_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+GTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
+GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
+TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
+TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
+GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
+GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
+CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
+GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
+GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
+TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
+CATGCCGAGATACGTCGCTGGCGCTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
+CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
+AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
+>GEN4.1111.00001.0001i_00007 261 NA | hypothetical protein | NA | NA | NA
+ATGGCTGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
+GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
+CGTCAACTTAGCGCGTGGGAGGCCGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
+ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGTC
+GGTTATCGACTCGAAGGTTGA
+>GEN4.1111.00001.0001i_00008 582 NA | hypothetical protein | NA | NA | NA
+ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
+CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTCGAGATGATCGTCCCTCAACTA
+CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
+GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
+TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
+GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
+CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
+CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
+TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
+TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
+>GEN4.1111.00001.0001b_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+ATGAATAGCGGGGGAATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAA
+CTGCCCGGCTCGCTCTCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCC
+GGATCGGCAATTGCCGCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGC
+GAAGGTTACGATCGCGGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATG
+TTAATTCCGCCCACCACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATT
+GCCGCTCTGTTCGCCGGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTG
+GTCACGCTGGTGGTCGCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGC
+ATGGCGCTAAAAGTTGCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATCGTC
+GGCGGCATTGTGCAGGGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTAT
+ACATTATTGTTGACGATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATT
+TTGCTCCAGACAGTGGTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCG
+ATGTCCTTCTCGATGTCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGT
+ATTTCCGCCAATAAACTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGC
+GCATTTATGGATATCGGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATG
+GCTAAACTGGGCGTCGATCCGGTGCATTTTGGCATTATCATGATCTATAACCTGGCGATT
+GGCACCATTACGCCGCCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTC
+AAAGTTGAGGAAGTGATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTG
+TTATTAATTACCTACATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATG
+TAA
diff --git a/Examples/input_files/pan-input/Genes/GENO.0321.00001.gen b/Examples/input_files/pan-input/Genes/GENO.0321.00001.gen
new file mode 100644
index 0000000000000000000000000000000000000000..7e6ce6accb014d8cee7e5004693b0fe096ccff7f
--- /dev/null
+++ b/Examples/input_files/pan-input/Genes/GENO.0321.00001.gen
@@ -0,0 +1,169 @@
+>GENO.0321.00001.0001b_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
+ATGAGTGAGGCTGAAGCCCGCCCGACTAACTTTATTCGTCAGATTATTGATGAAGATCTG
+GCGAGTGGTAAACATACCACTGTCCATACCCGTTTTCCGCCGGAGCCGAATGGCTATCTG
+CATATCGGCCACGCGAAATCTATCTGCCTGAACTTTGGCATCGCGCAAGATTATCAGGGC
+CAGTGCAACCTGCGTTTCGATGACACCAACCCGGTAAAAGAAGATATCGAGTACGTTGAT
+TCGATCAAAAACGACGTCGAGTGGTTAGGCTTTCACTGGTCTGGCGATATTCGCTACTCC
+TCCGATTACTTTGACCAACTGCACGCCTATGCGGTCGAGCTAATCAATAAAGGCCTGGCC
+TATGTTGATGAGCTGACGCCGGAGCAGATCCGTGAATACCGCGGTACGCTGACCGCGCCG
+GGTAAAAACAGCCCGTTCCGCGATCGCAGCGTCGAAGAGAACCTCGCGCTATTTGAAAAA
+ATGCGTACCGGCGGTTTTGAAGAGGGTAAAGCCTGTCTGCGCGCTAAAATCGACATGGCG
+TCGCCGTTTATCGTGATGCGCGATCCGGTGCTGTATCGCATTAAATTCGCCGAGCATCAT
+CAGACTGGCAACAAGTGGTGCATCTATCCGATGTACGACTTTACTCACTGCATCAGCGAT
+GCGCTGGAAGGCATTACTCATTCTCTGTGTACGCTGGAGTTCCAGGATAACCGTCGTCTG
+TACGACTGGGTGCTGGACAACATCACCATTCCGGTTCACCCGCGCCAGTACGAATTCTCG
+CGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGCTGAACCTGCTGGTGACCGAC
+AAACACGTCGAAGGTTGGGACGATCCGCGTATGCCGACTATTTCCGGTCTGCGCCGTCGC
+GGCTATACCGCGGCTTCTATTCGTGAGTTCTGCAAACGCATCGGCGTCACCAAGCAGGAC
+AACACTATTGAGATGGCGTCGCTGGAATCCTGCATTCGCGAAGATCTGAACGAAAACGCG
+CCGCGCGCGATGGCGGTAATCGATCCGGTAAAACTGGTTATCGAAAATTACCCGCAGGGT
+GAGAGCGAAATGGTTACCATGCCTAACCATCCGAATAAACCGGAGATGGGCAGCCGTGAA
+GTGCCGTTTAGCGGTGAGATCTGGATCGATCGCGCAGATTTCCGCGAAGAAGCGAACAAA
+CAGTACAAACGTCTGGTGATGGGCAAAGAAGTGCGTCTGCGTAATGCCTACGTCATTAAA
+GCGGAGCGCGTAGAGAAGGATGCCGAAGGGAATATCACCACCATCTTCTGTACCTATGAT
+GCTGATACGCTGAGTAAAGATCCGGCTGACGGGCGTAAAGTGAAAGGCGTAATCCACTGG
+GTTAGCGCAGCACATGCGCTGCCGATTGAAATTCGTCTCTACGACCGTCTGTTCAGCGTG
+CCGAATCCGGGCGCCGCGGAGGACTTCCTGTCTGTTATCAACCCCGAATCATTAGTGATT
+AAGCAGGGGTATGGCGAGCCGTCGCTGAAAGCGGCGGTAGCAGGAAAAGCTTTCCAGTTT
+GAACGTGAAGGCTACTTCTGCCTCGACAGCCGCTATGCAACGGCCGATAAGCTGGTCTTT
+AACCGCACCGTGGGCCTGCGTGATACCTGGGCGAAAGCGGGCGAGTAA
+>GENO.0321.00001.0001b_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+ATGAAAGCGCTACTGTGGCTGGTGGGTCTCGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
+AAAGGAATTATCGATAAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
+TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
+GCGACGTTAACGGGTCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
+TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
+GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
+GAAAATCGTGGTTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
+CAAATTCAGGCATTGATTCCGTTAGCGAAGGATATTATCGCGCGCTATAACATCAAACCG
+CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
+TTCCCGTGGCGCGAGCTGGCGGCGCAGGGGATTAGCGCCTGGCCTGACGCCCAGCGTGTG
+GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
+TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCACGCGAGCAGCAGCGG
+GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
+GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
+>GENO.0321.00001.0002b_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+ATGCCGCACTTTATTGCTGAATGTACTGAAAATATTCGCGAGCAGGCTGATTTACCCGGC
+CTGTTCAGCAAGGTAAACGAGGCGCTGGCCGCCAGCGGGATTTTCCCCATCGGCGGTATC
+CGCAGTCGCGCCCACTGGCTGGATACCTGGCAGATGGCTGACGGTAAGCATGATTACGCG
+TTTGTGCATATGACGCTGAAAATCGGCGCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTT
+GGCGAAATGCTGTTTGGGCTGATTAAAGCCCACTTCGCCGACCTGATGGAGAACCGCTAT
+CTGGCGCTGTCGTTTGAGATTGCCGAGCTACATCCGACGCTCAATTACAAACAAAACAAC
+GTACACGCGTTATTTAAATAG
+>GENO.0321.00001.0002i_00004 1410 NA | hypothetical protein | NA | NA | NA
+ATGAGCATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTT
+GCTGTTCTTCCTTTTCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTC
+GATATTAAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGAC
+GGACAGACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACG
+ATTCCGGCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGG
+TTTATTTTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTG
+ACGCTGGATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGC
+CCCGTCGCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATC
+GATGACATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAA
+ATGGATGGCGCGCGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAG
+TGGAATGTCGCGATTCACGACCGCGACATCCTGATTTCCGATCATGTCATCGAACGCATT
+AATTGTACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTAT
+GACAACAGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGA
+TCTGATTGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTC
+AAAGCCAAAAACATCACGCCCGGTTTCAGTAAAAATGCGGGTATTGATAACGCAACGATC
+GCAATTTATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGG
+ATGCTCATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAA
+TTAAACGCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATT
+TCCTCCGGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACG
+CTGGAACTGCATAATCAACCGCAGCACCTCTTTCTGCGCAATATCAACGTGATGCAAACT
+TCAGCGATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTACGTGGTCAA
+TTTATGGCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAAC
+GGGCAGAGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTG
+AATTTTTCGCTGCCGAAGCGGGGAGGGTAA
+>GENO.0321.00001.0002i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
+CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
+GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGGC
+GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGATGGGCAGCTCAAA
+GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
+TTCAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
+CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
+ATTGATGAGCGCGCTCAGGGCAAATATCCCGTCCATCTCTCCGGCGGCCAACAGCAGCGC
+GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACA
+TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
+GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGCTCGCCATGTCTCTTCG
+CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGTGATCCGGAGCAGGTGTTC
+GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
+>GENO.0321.00001.0002i_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+ATGTTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTG
+AACATCCAAAGCTGGAGTCCTCGCGACTTCGCGCATGACCGGCACCGTACCGTGGACGAC
+CGTCCTTACGGCGGCGGACCGGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATT
+CACGCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGA
+CGCAAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTG
+TGTGGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGG
+TCAATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCC
+GTCGCCCGGTTTATACCGGGGGTTCTGGGGCATGAGGCATCAGCAATCGAAGATTCGTTT
+GCTGATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAA
+GTACCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAG
+TCGCTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAA
+GAGCAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACAT
+GATGGGATGGCATAG
+>GENO.0321.00001.0002i_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+ATGATGGGATGGCATAGCCGTCATATGGGCTCTCAGAGGAGACGCGCTAATGCGCAGTAC
+GTGTTTATTGGCATAGTTAGCCTGTTTCCTGAAATGTTCCGCGCAATTACCGATTACGGG
+GTAACTGGCCGGGCAGTAAAAAAAGGCCTGCTGAACATCCAAAGCTGGAGTCCTCGCGAC
+TTCGCGCATGACCGGCACCGTACCGTGGACGACCGTCCTTACGGCGGCGGACCGGGGATG
+TTAATGATGGTGCAACCCTTGCGGGACGCCATTCACGCAGCAAAAGCCGCGGCAGGTGAA
+GGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGCAAGCTTGATCAAGCGGGCGTTAGC
+GAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGTGGTCGCTACGAAGGCGTAGATGAG
+CGCGTAATTCAGACCGAAATTGACGAAGAATGGTCAATTGGCGATTACGTTCTCAGCGGT
+GGCGAACTACCGGCAATGACGCTGATTGACTCCGTCGCCCGGTTTATACCGGGGGTTCTG
+GGGCATGAGGCATCAGCAATCGAAGATTCGTTTGCTGATGGGTTGCTGGATTGTCCGCAC
+TATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTACCGCCAGTATTGCTGTCGGGAAAC
+CATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCGCTGGGCCGAACCTGGCTTAGAAGA
+CCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAGCAAGCAAGGTTGCTGGCGGAGTTC
+AAAACAGAACACGCACAACAGCAGCATAAACATGATGGGATGGCATAG
+>GENO.0321.00001.0002i_00008 465 NA | hypothetical protein | NA | NA | NA
+ATGAAGTTTGTTGCGCCCGAACAGGCACCGGAACAGGCGGAGGTCATCAAAAATACGCCG
+TTCTGGCCTGATGTGGACCTGTCGGAATTTCGCAGTGTGATGCGCACTGACGGCACGGTG
+ACGCAGCCGCGTTTAAAGCAGGTCGTGCTGACGGCGATCTCTGAGGTTAACGCTGAGCTG
+TACGACTTCCGCAACCGTCAGCAGATGCTGGGCTGGCGGACACTTGCTGAGGTTCCCGCA
+GAAATGCTGGACGGTAAAAGCGAGCGTATCCGGCACTACCACAACGCTGTTTTTTGCTGG
+GCGCGCGCTGTGCTTAATGAGCGTTATCAGGACTATGACGCCACGGCGTCAGGCGTGAAG
+CGAGGGGAGGAGCTGGCGGAGGCCAGCGGCGATCTGTGGCGTGATGCCCGCTGGGCCATC
+AGCCGGGTGCAGGATGTACCGCACTGTACGGTGGAGCTTATCTGA
+>GENO.0321.00001.0002i_00009 261 NA | hypothetical protein | NA | NA | NA
+ATGGCCGGGTTGCACGCGCCATATGCATATAGCGCGCATCATGCGGTGAATTTCTGTTCT
+GAGTATAAACGTGGCTTTGTATTGGGTTTTACACACCGTATGTTCGAAAAGACCGGCGAT
+CGTCAACTTAGCGCGTGGGAGGCTGGAATTCTGACGCGTCGCTATGGTCTGGATAAAGAA
+ATGGTGATGGATTTCTTTAAAGAGAATCATTCCGGGATGGCGGTTCGCTTCTTTATGGCC
+GGTTATCGACTCGAAGGTTGA
+>GENO.0321.00001.0002i_00010 582 NA | hypothetical protein | NA | NA | NA
+ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
+CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAGCTG
+CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAATCTCTCGTGCTTGAGCATGGCGGT
+GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
+TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
+GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
+CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
+CTACTGCAACAGACGGGCGATGAAGTGCTGTATTACCGCCAGGCGGTGGCATATTACGCC
+TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
+TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
+>GENO.0321.00001.0002b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
+ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
+CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
+TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
+ATTGCCGCCCGGCTGGTCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGCTCGCTC
+TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCGATTGCC
+GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
+GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
+ACGGCTTTTATCCTTTACGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
+GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTGGTC
+GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGTATGGCGCTAAAAGTT
+GCCGTTGAGGCCATTCCCAGCCTGCTGCTGATCGTGATTATTGTCGGCGGCATTGTGCAG
+GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
+ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
+GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCGATG
+TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
+CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATT
+GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCAATCATGGCTAAACTGGGCGTC
+GATCCGGTGCATTTCGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
+CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
+ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
+ATTCCGGAAATCACACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
diff --git a/Examples/input_files/pan-input/Genes/GENO.1216.00002.gen b/Examples/input_files/pan-input/Genes/GENO.1216.00002.gen
new file mode 100644
index 0000000000000000000000000000000000000000..e58bf05f8b869e5db8d0cc48d26f9110b29b1fb7
--- /dev/null
+++ b/Examples/input_files/pan-input/Genes/GENO.1216.00002.gen
@@ -0,0 +1,158 @@
+>GENO.1216.00002.0001b_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
+AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
+TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
+GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
+TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
+GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
+GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
+CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
+CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
+TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
+GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
+TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
+GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
+GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
+>GENO.1216.00002.0001i_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+ATGAGAGCGCTACTGTGGCTGGTGGGTCTTGCGTTGCTGTTAACAGGCTGCGCGAGCGAA
+AAAGGAATTATCGATGAAGAGGGATATCAGCTTGATACCCGACATCGGGCGCAGGCGGCC
+TATCCGCGCATTAAAGTCCTGGTGATTCACTATACGGCGGAAAACTTTGACGTTTCGCTG
+GCGACGTTAACGGGCCGCAACGTCAGTTCGCATTACCTGATTCCCGCAACCCCGCCATTA
+TATGGCGGTAAACCGCGCATCTGGCAACTGGTGCCGGAACAGGATCAGGCCTGGCATGCG
+GGCGTCAGTTTCTGGCGAGGCGCCACGCGTCTCAATGATACGTCTATTGGCATTGAGCTG
+GAAAATCGCGGCTGGCGAATGTCCGGCGGGGTGAAATCTTTCGCGCCGTTTGAATCCGCG
+CAAATTCAGGCATTGATTCCGTTAGCGAAGGACATTATCGCGCGCTATGACATCAAACCG
+CAGAATGTGGTGGCCCATGCGGATATCGCGCCGCAGCGTAAAGACGATCCCGGCCCGCGC
+TTCCCGTGGCGCGAGCTGGCGGCACAGGGGATTGGCGCCTGGCCTGACGCCCAGCGTGTG
+GCGTTTTATCTGGCTGGACGCGCGCCGTATACGCCAGTCGATACCGCAACGGTGCTTGCG
+TTACTCTCGCGCTATGGCTATGAAGTCAAAGCCGATATGACGGCGCGCGAGCAACAGCGG
+GTGATTATGGCGTTCCAGATGCACTTCCGTCCGGCGCAATGGAACGGTATCGCAGATGCC
+GAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAA
+>GENO.1216.00002.0001i_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+ATGCCGAAACGCAGGCGATTGCCGAAGCATTACTGGAGAAGTACGGCCAGGATTAACAGG
+GCGCGGTATCGCGAGGACTCTCTCTTCGAGGACATGCCGCACTTTATTGCTGAATGTACT
+GAAAATATTCGCGAGCAGGCTGATTTACCCGGCCTGTTCAGCAAGGTAAACGAGGCGCTG
+GCCGCCAGCGGGATTTTCCCCATCGGCGGTATCCGCAGTCGCGCCCACTGGCTGGATACC
+TGGCAGATGGCTGACGGTAAGCATGATTACGCGTTTGTGCATATGACGCTGAAAATCGGC
+GCCGGGCGCAGCCTGGAGAGCCGTCAGGAAGTCGGCGAAATGCTGTTCGGGCTGATTAAA
+GCCCACTTCGCCGACCTGATGGAGAACCGCTATCTGGCGCTGTCGTTTGAGATTGCCGAG
+TTACATCCAACGCTCAATTACAAACAAAACAACGTACACGCGTTATTTAAATAG
+>GENO.1216.00002.0001i_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
+ATGAGCGCGCTATTTCTGGCCATCCCGTTAACCATTTTTGTGTTGTTTGTGTTACCGATT
+TGGCTGTGGCTGCATTACAGCAACCGCGCCGGTCGGGGAGAACTGTCGCAAAGCGAGCAG
+CAACGCTTACTGCAACTCACAGACGACGCGCAACGTATGCGCGAGCGCATTCAGGCGCTG
+GAAGACATTCTTGATGCAGAGCATCCGAACTGGAGAGAGCGCTAA
+>GENO.1216.00002.0001i_00005 1404 NA | hypothetical protein | NA | NA | NA
+ATGCCCGCGACTAAATTCTCCCGACGTACCCTCCTGACGGCAGGTTCTGCGCTTGCTGTT
+CTTCCTTTCCTGCGCGCCTTGCCGGTACAGGCGCGTGAACCTCGCGAGACCGTCGATATT
+AAGGATTATCCGGCGGATGACGGTATCGCCTCGTTCAAACAGGCCTTCGCCGACGGACAG
+ACCGTGGTCGTACCGCCAGGATGGGTGTGTGAAAATATCAATGCGGCGATAACGATTCCG
+GCGGGAAAAACGCTGCGGGTACAGGGCGCGGTGCGTGGGAATGGCCGGGGACGGTTTATT
+TTGCAGGACGGGTGTCAGGTGGTGGGGGAGCAGGGCGGCAGTCTGCACAATGTGACGCTG
+GATGTTCGCGGGTCGGACTGTGTGATTAAAGGCGTGGCGATGAGCGGCTTTGGCCCCGTC
+GCGCAAATTTTCATCGGTGGTAAGGAACCGCAGGTGATGCGTAATCTCATTATCGATGAC
+ATCACCGTTACCCACGCCAACTACGCCATTCTCCGCCAGGGATTTCATAACCAAATGGAC
+GGCGCGAGGATTACGCATAGCCGCTTTAGCGATTTACAGGGGGACGCCATTGAGTGGAAT
+GTCGCGATTCACGACCGCGATATCCTGATTTCCGATCATGTCATCGAACGCATTGATTGT
+ACCAATGGCAAAATCAACTGGGGGATCGGCATCGGGCTGGCGGGTAGCACCTATGACAAC
+AGTTATCCTGAAGACCAGGCAGTAAAAAACTTTGTGGTGGCCAATATTACCGGATCTGAT
+TGCCGACAGCTTGTGCACGTAGAAAATGGCAAACATTTCGTCATTCGCAATGTCAAAGCC
+AAAAACATCACGCCCGATTTCAGTAAAAATGCGGGTATTGATAACGCAACGATCGCAATT
+TATGGCTGTGATAATTTCGTCATTGATAATATTGATATGACGAATAGTGCCGGGATGCTC
+ATCGGCTATGGCGTCGTTAAAGGAAAATACCTGTCAATTCCGCAAAACTTTAAATTAAAC
+GCTATTCGGTTGGATAATCGCCAGGTTGCTTATAAATTACGCGGCATTCAAATTTCCTCC
+GGCAACACCCCCTCTTTTGTCGCCATCACCAATGTACGGATGACGCGTGCTACGCTGGAA
+CTGCATAATCAACCGCAGCACCTCTTCCTGCGTAATATCAACGTGATGCAAACTTCAGCG
+ATTGGCCCGGCGTTAAAAATGCATTTCGATTTGCGTAAAGATGTCCGTGGTCAATTTATG
+GCCCGCCAGGACACGCTGCTTTCCCTCGCTAATGTTCATGCCATCAATGAAAACGGGCAG
+AGTTCCGTGGATATCGACAGGATTAATCACCAAACCGTGAATGTCGAAGCAGTGAATTTT
+TCGCTGCCGAAGCGGGGAGGGTAA
+>GENO.1216.00002.0001i_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+ATGTCAGAAAATAAATTACACGTTATCGATTTGCACAAACGCTACGGCGGTCATGAAGTG
+CTGAAAGGGGTATCGCTGCAGGCCCGCGCCGGAGATGTGATTAGCATCATCGGCTCGTCC
+GGCTCCGGTAAAAGCACTTTTTTGCGCTGTATTAACTTCCTCGAAAAACCGAGCGAAGAC
+GCGATTATCGTGAACGGTCAGAACATTAATCTGGTGCGCGACAAAGACGGGCAGCTCAAA
+GTGGCGGATAAAAATCAGCTACGCTTGTTGCGTACCCGCCTGACGATGGTGTTTCAGCAC
+TTTAACCTCTGGAGCCACATGACGGTGCTGGAAAATGTGATGGAAGCGCCGATTCAGGTA
+CTGGGATTAAGCAAGCACGACGCGCGCGAGCGGGCGTTGAAATATCTGGCGAAGGTGGGG
+ATTGATGAGCGCGCTCAGGGCAAATATCCCGTTCATCTCTCCGGTGGCCAACAGCAGCGC
+GTTTCTATTGCGCGCGCGCTGGCGATGGAACCTGACGTTTTACTGTTCGATGAACCCACT
+TCGGCGCTCGATCCTGAACTGGTCGGCGAAGTGTTGCGCATCATGCAACAACTGGCGGAA
+GAAGGCAAAACGATGGTGGTGGTCACGCATGAAATGGGCTTCGTTCGCCATGTCTCTTCG
+CACGTTATTTTTCTGCATCAGGGGAAAATTGAAGAAGAGGGCGATCCGGAGCAGGTGTTC
+GGCAATCCGCAAAGCCCGCGTTTACAGCAATTCCTGAAAGGCTCGCTGAAATAA
+>GENO.1216.00002.0001i_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+ATGCGCGCGATATATCGGCGATGCGTGTTTATTGGCATCGTTAGCCTGTTTCCTGAAATG
+TTCCGCGCAATTACCGATTACGGGGTAACTGGCCGGGCAGTAAAAAATGGCCTGCTGAAC
+ATCCAAAGCTGGAGTCCTCGCGACTTCACGCATGACCGGCACCGTACCGTGGACGATCGT
+CCTTACGGCGGCGGACCAGGGATGTTAATGATGGTGCAACCCTTGCGGGACGCCATTCAC
+GCAGCAAAAGCCGCGGCAGGTGAAGGCGCTAAAGTGATTTATCTGTCGCCTCAGGGACGC
+AAGCTTGATCAAGCGGGCGTTAGCGAGCTGGCCACGAATCAGAAGCTTATTCTGGTGTGT
+GGTCGCTACGAAGGCGTAGATGAGCGCGTAATTCAGACCGAAATTGACGAAGAATGGTCA
+ATTGGCGATTACGTTCTCAGCGGTGGCGAACTACCGGCAATGACGCTGATTGACTCCGTC
+GCCCGGTTTATACCGGGAGTTCTGGGGCATGAAGCATCAGCAATCGAAGATTCGTTTGCT
+GATGGGTTGCTGGATTGTCCGCACTATACGCGCCCTGAAGTGTTAGAGGGGATGGAAGTA
+CCGCCAGTATTGCTGTCGGGAAACCATGCTGAGATACGTCGCTGGCGTTTGAAACAGTCG
+CTGGGCCGAACCTGGCTTAGAAGACCTGAACTTCTGGAAAACCTGGCTCTGACTGAAGAG
+CAAGCAAGGTTGCTGGCGGAGTTCAAAACAGAACACGCACAACAGCAGCATAAACATGAT
+GGGATGGCATAG
+>GENO.1216.00002.0001b_00008 288 NA | hypothetical protein | NA | NA | NA
+ATGAATAATCATTTTGGGAAAGGGTTAATGGCCGGGTTGCACGCGCCATATGCATATAGC
+GCGCATCATGCGGTGAATTTCTGTTCTGAGTATAAACGTGGCTTTGTATTGGGTTTTACA
+CACCGTATGTTCGAAAAGACCGGCGATCGTCAACTTAGCGCGTGGGAGGCTGGAATTCTG
+ACGCGTCGCTATGGTCTGGATAAAGAAATGGTGATGGATTTCTTTAAAGAGAATCATTCC
+GGGATGGCGGTTCGCTTCTTTATGGCCGGTTATCGACTCGAAGGTTGA
+>GENO.1216.00002.0002b_00009 582 NA | hypothetical protein | NA | NA | NA
+ATGTCTACGCTTCTCTATTTGCACGGATTCAACAGTTCCCCTCGCTCGGCAAAAGCGTGC
+CAGCTAAAAAACTGGCTGGCGGAGCGTCATCCGCATGTTGAGATGATCGTCCCTCAACTA
+CCGCCGTATCCTGCCGATGCGGCGGAGTTGCTGGAGTCTCTCGTGCTTGAGCATGGCGGT
+GCGCCATTAGGGCTGGTAGGATCGTCGCTGGGTGGTTATTACGCCACCTGGCTGTCGCAA
+TGTTTTATGCTGCCGGCTGTGGTGGTGAATCCCGCCGTGCGGCCCTTTGAATTACTGACC
+GACTATCTCGGTCAGAACGAGAACCCCTACACCGGGCAGCAATATGTGCTAGAGTCTCGC
+CATATTTATGATCTTAAAGTCATGCAGATTGACCCGCTGGAAGCGCCGGACCTGATCTGG
+CTACTGCAACAGACGGGCGATGAAGTGCTGGATTACCGCCAGGCGGTGGCATATTACGCC
+TCCTGCCGTCAGACAGTGACCGAGGGTGGTAATCACGCATTCACGGGCTTCGAAGATTAT
+TTCAACCAGATTGTCGATTTTCTTGGACTGCACAGTTGCTGA
+>GENO.1216.00002.0002b_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+ATGATTGACCCTATTTTTGCGTCCTGTACGCTAATTGCCGTCTTTGTTGTTTTACTGGCC
+ATGGGCGCGCCTATCGGGATCTGCATCGTTATCGCCTCTTTCAGCACCATGATGCTGGTA
+CTGCCTTTCGATATTTCGATGTTCGCCACCGCGCAAAAAATGTTCTCCAGCCTGGACAGT
+TTTGCCTTGCTGGCCGTGCCGTTCTTCGTTTTGTCCGGGGTGATCATGAATAGCGGGGGA
+ATTGCCGCCCGGCTGATCAATTTTGCCAAACTGTTTACTGGCAAACTGCCCGGTTCGCTC
+TCTTATACCAACATCGTCGGCAATATGATGTTCGGTGCAATTTCCGGATCGGCAATTGCC
+GCCTCAACCTCCATCGGCGGCGTGATGGTGCCGATGAGCGCGCGCGAAGGTTACGATCGC
+GGCTTTGCGGCCGCGGTGAATATCGCCTCCGCGCCGACGGGAATGTTAATTCCGCCCACC
+ACGGCTTTTATCCTTTATGCGCTGGCAAGCGGGGGAACATCGATTGCCGCTCTGTTCGCC
+GGCGGTCTGGTCGCGGGAGTGCTGTGGGGCGTTGGCTGTATGCTGGTCACGCTGGTAGTC
+GCTAAGCGTCGAAATTATCGGGTTTTCTTCACCGTCCAAAAAGGCATGGCGCTAAAAGTT
+GCCGTTGAGGCCATTCCCAGCCTGTTACTGATCGTGATTATCGTCGGCGGCATTGTGCAG
+GGGATTTTCACCGCCATTGAAGCCTCCGCGATTGCCGTGGTGTATACGTTATTGCTGACG
+ATGGTGTTTTACCGCACGCTGAAAATTAAGGATTTGCCTTCGATTTTGCTCCAGACAGTG
+GTAATGACCGGGGTCATCATGTTCCTGCTGGCAACCTCTTCGGCGATGTCCTTCTCAATG
+TCGATCACCAATATTCCTGCGGCGCTGAGCGATATGATCCTCGGTATTTCCGCCAATAAA
+CTGGTTATCCTGTTAGTCATTACCGTCTTTTTGTTGATTATCGGCGCATTTATGGATATC
+GGTCCGGCCATTCTGATTTTTACCCCGATTCTGCTGCCGATCATGGCTAAACTGGGCGTC
+GATCCGGTGCATTTGGGCATTATCATGATCTATAACCTGGCGATTGGCACCATTACGCCG
+CCAGTTGGCAGTGGTTTATATGTCGGGGCGAGCGTCGGTAAGGTCAAAGTTGAGGAAGTG
+ATTAAACCGTTGCTGCCTTTTTACGGCGCGATTATCGGCGTTCTGTTATTAATTACCTAC
+ATTCCGGAAATCATACTGTTCTTACCCCGTCTACTGGGCATCATGTAA
+>GENO.1216.00002.0003b_00011 255 NA | hypothetical protein | NA | NA | NA
+ATGATAATTAATGGGAAATTAATTAAAGCAAAAGACTTAGCTAAGGCTGCAGGTGTATCT
+CGTTCAACAGTGATTAAATATTACGGCATTAGCCGTGAGAATTACGAAAGGGTAGCAACT
+GAAAGAAGGAAGCTTGCTTTTGAACTAAGAGCATCAGGTTTAAAATGGAAAGAAGTTGCT
+GAAAAAATGAACACGACAAAATATAGCGCAATTGCATATTATAGACGATATTTAGCATTA
+GAGAAAAACAAATAA
+>GENO.1216.00002.0003b_00012 780 NA | IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
+ATGGTCGAACTGCAACATCAACGGCTGATGGTGCTTGCCGAACAGCTCCAGCTGGACAGT
+CTTATCGGCGCAGCGCCGGCGCTGTCGCAACAGGCGGTGGATCAGGAATGGAGCTACATG
+GACTTCCTGGAGCACCTGTTACATGAGGAGAAACTGGCCCGGCATCAGCGTAAACAGGCG
+ATGTACACGCGGATGGCAGCCTTCCCGGCGGTAAAGACGTTCGAGGAGTACGACTTCACC
+TTCGCCACCGGCGCTCCTCAGAAGCAAATCCAGTCGCTGCGATCCCTGAGCTTCATAGAG
+CGTAACGAAAACATCGTGTTGCTGGGGCCATCGGGCGTGGGAAAAACGCATCTGGCGATA
+GCCATGGGCTACGAAGCAGTACGGGCGGGCATCAAGGTTCGCTTCACAACAGCAGCGGAC
+CTGCTGCTACAGCTGTCCACTTCACAGCGTCAGGGCCGTTACAAAACGACTCTCAATCGT
+GGTGTCATGGCCCCGAAGCTGCTTATCATCGATGAAATAGGTTATCTGCCGTTCAGTCAG
+GAGGAAGCCAAGCTGTTCTTCCAGGTCATCGCCAAACGTTACGAGAAGAGCGCGATGATC
+CTGACCTCCAACCTGCCGTTCGGGCAGTGGGATCAGACGTTCGCCGGTGATGCAGCGCTG
+ACATCGGCGATGCTGGACCGGATCTTACATCACTCACACGTCGTGCAAATAAAAGGGGAA
+AGCTATCGACTGAAGCAGAAACGAAAGGCCGGGGTTATAGCTGAAGCTAATCCTGAGTAA
diff --git a/Examples/input_files/pan-input/LSTINFO-list_genomes.lst b/Examples/input_files/pan-input/LSTINFO-list_genomes.lst
new file mode 100644
index 0000000000000000000000000000000000000000..3b4150bc114612a9d45b684c710f91de4cc0dae1
--- /dev/null
+++ b/Examples/input_files/pan-input/LSTINFO-list_genomes.lst
@@ -0,0 +1,4 @@
+gembase_name	orig_name	to_annotate	gsize	nb_conts	L90
+GEN4.1111.00001	genome4.fst	Examples/input_files/pan-init-files/tmp_files/genome4.fst_prokka-split5N.fna	7134	1	1
+GENO.0321.00001	genome1.fst	Examples/input_files/pan-init-files/tmp_files/genome1.fst_prokka-split5N.fna	9808	2	2
+GENO.1216.00002	genome3-chromo.fst-all.fna	Examples/input_files/pan-init-files/tmp_files/genome3-chromo.fst-all.fna_prokka-split5N.fna	8817	3	3
diff --git a/Examples/input_files/pan-input/Proteins/GEN4.1111.00001.prt b/Examples/input_files/pan-input/Proteins/GEN4.1111.00001.prt
new file mode 100644
index 0000000000000000000000000000000000000000..841d437809448de6299df1faef13f9da3d26df92
--- /dev/null
+++ b/Examples/input_files/pan-input/Proteins/GEN4.1111.00001.prt
@@ -0,0 +1,52 @@
+>GEN4.1111.00001.0001b_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GEN4.1111.00001.0001i_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
+FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
+VHALFK
+>GEN4.1111.00001.0001i_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
+MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
+KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
+HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
+DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
+TRPVPASKGDTFHVDYGNMGAISCRFV
+>GEN4.1111.00001.0001i_00004 1404 NA | hypothetical protein | NA | NA | NA
+MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
+TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
+DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
+GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
+SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
+YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
+GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
+ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GEN4.1111.00001.0001i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GEN4.1111.00001.0001i_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
+LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
+RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
+YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
+KTEHAQQQHKHDGMA
+>GEN4.1111.00001.0001i_00007 261 NA | hypothetical protein | NA | NA | NA
+MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
+MVMDFFKENHSGMAVRFFMVGYRLEG
+>GEN4.1111.00001.0001i_00008 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GEN4.1111.00001.0001b_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
+EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
+VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
+TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
+ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
+GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
diff --git a/Examples/input_files/pan-input/Proteins/GENO.0321.00001.prt b/Examples/input_files/pan-input/Proteins/GENO.0321.00001.prt
new file mode 100644
index 0000000000000000000000000000000000000000..209d0341635283d5ae2f4c84f935bb820e54b15d
--- /dev/null
+++ b/Examples/input_files/pan-input/Proteins/GENO.0321.00001.prt
@@ -0,0 +1,69 @@
+>GENO.0321.00001.0001b_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
+MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
+QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
+YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
+SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
+YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
+GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
+ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
+AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
+PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
+NRTVGLRDTWAKAGE
+>GENO.0321.00001.0001b_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.0321.00001.0002b_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
+FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
+VHALFK
+>GENO.0321.00001.0002i_00004 1410 NA | hypothetical protein | NA | NA | NA
+MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
+GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
+TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
+MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
+DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
+AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
+SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
+FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GENO.0321.00001.0002i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GENO.0321.00001.0002i_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
+HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
+SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
+VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
+DGMA
+>GENO.0321.00001.0002i_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
+FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
+ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
+GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
+PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA
+>GENO.0321.00001.0002i_00008 465 NA | hypothetical protein | NA | NA | NA
+MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
+YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
+RGEELAEASGDLWRDARWAISRVQDVPHCTVELI
+>GENO.0321.00001.0002i_00009 261 NA | hypothetical protein | NA | NA | NA
+MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
+MVMDFFKENHSGMAVRFFMAGYRLEG
+>GENO.0321.00001.0002i_00010 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GENO.0321.00001.0002b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
+FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
+ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
+GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
+GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
+SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
+DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
+IPEITLFLPRLLGIM
diff --git a/Examples/input_files/pan-input/Proteins/GENO.1216.00002.prt b/Examples/input_files/pan-input/Proteins/GENO.1216.00002.prt
new file mode 100644
index 0000000000000000000000000000000000000000..7c1048821cbe65e197fbc2c0672bcffe010aa868
--- /dev/null
+++ b/Examples/input_files/pan-input/Proteins/GENO.1216.00002.prt
@@ -0,0 +1,66 @@
+>GENO.1216.00002.0001b_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.1216.00002.0001i_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.1216.00002.0001i_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
+AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
+AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK
+>GENO.1216.00002.0001i_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
+MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
+EDILDAEHPNWRER
+>GENO.1216.00002.0001i_00005 1404 NA | hypothetical protein | NA | NA | NA
+MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
+TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
+DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
+GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
+SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
+YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
+GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
+ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GENO.1216.00002.0001i_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GENO.1216.00002.0001i_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
+PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
+GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
+DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
+QARLLAEFKTEHAQQQHKHDGMA
+>GENO.1216.00002.0001b_00008 288 NA | hypothetical protein | NA | NA | NA
+MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
+TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG
+>GENO.1216.00002.0002b_00009 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GENO.1216.00002.0002b_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
+FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
+ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
+GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
+GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
+SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
+DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
+IPEIILFLPRLLGIM
+>GENO.1216.00002.0003b_00011 255 NA | hypothetical protein | NA | NA | NA
+MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLKWKEVA
+EKMNTTKYSAIAYYRRYLALEKNK
+>GENO.1216.00002.0003b_00012 780 NA | IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
+MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
+MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
+AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
+EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
+SYRLKQKRKAGVIAEANPE
diff --git a/Examples/input_files/pan-input/Proteins/GENO3.All.prt b/Examples/input_files/pan-input/Proteins/GENO3.All.prt
new file mode 100644
index 0000000000000000000000000000000000000000..97f24aea3e7de95bd89ac9630961b0e67ea8475c
--- /dev/null
+++ b/Examples/input_files/pan-input/Proteins/GENO3.All.prt
@@ -0,0 +1,187 @@
+>GEN4.1111.00001.0001b_00001 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GEN4.1111.00001.0001i_00002 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
+FVHMTLKIGTGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
+VHALFK
+>GEN4.1111.00001.0001i_00003 804 hpcG | 2-oxo-hept-4-ene-1,7-dioate hydratase | 4.2.1.163 | similar to AA sequence:UniProtKB:P42270 | NA
+MLDKQTHTLIAQRLNQAEKQREQIRAVSLDYPNITIEDAYAVQREWVNIKIAEGRTLKGH
+KIGLTSKAMQASSQISEPDYGALLDDMFFHDGGDIPTDRFIVPRIEVELAFVLAKPLRGP
+HCTLFDVYNATDYVIPALELIDARSHNIDPETQRPRKVFDTISDNAANAGVILGGRPIKP
+DELDLRWISALLYRNGVIEETGVAAGVLNHPANGVAWLANKLAPYDVQLEAGQIILGGSF
+TRPVPASKGDTFHVDYGNMGAISCRFV
+>GEN4.1111.00001.0001i_00004 1404 NA | hypothetical protein | NA | NA | NA
+MPVNKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
+TVVLPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
+DVRGSDCVIKGVTMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
+GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
+SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
+YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
+GNIPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
+ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GEN4.1111.00001.0001i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GEN4.1111.00001.0001i_00006 768 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGM
+LMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDE
+RVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPH
+YTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEF
+KTEHAQQQHKHDGMA
+>GEN4.1111.00001.0001i_00007 261 NA | hypothetical protein | NA | NA | NA
+MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
+MVMDFFKENHSGMAVRFFMVGYRLEG
+>GEN4.1111.00001.0001i_00008 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GEN4.1111.00001.0001b_00009 1083 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIAASTSIGGVMVPMSAR
+EGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFAGGLVAGVLWGVGCML
+VTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQGIFTAIEASAIAVVY
+TLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSMSITNIPAALSDMILG
+ISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGVDPVHFGIIMIYNLAI
+GTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITYIPEITLFLPRLLGIM
+>GENO.0321.00001.0001b_00001 1668 glnS | Glutamine--tRNA ligase | 6.1.1.18 | similar to AA sequence:UniProtKB:P00962 | COG:COG0008
+MSEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYQG
+QCNLRFDDTNPVKEDIEYVDSIKNDVEWLGFHWSGDIRYSSDYFDQLHAYAVELINKGLA
+YVDELTPEQIREYRGTLTAPGKNSPFRDRSVEENLALFEKMRTGGFEEGKACLRAKIDMA
+SPFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRL
+YDWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRR
+GYTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYPQG
+ESEMVTMPNHPNKPEMGSREVPFSGEIWIDRADFREEANKQYKRLVMGKEVRLRNAYVIK
+AERVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPIEIRLYDRLFSV
+PNPGAAEDFLSVINPESLVIKQGYGEPSLKAAVAGKAFQFEREGYFCLDSRYATADKLVF
+NRTVGLRDTWAKAGE
+>GENO.0321.00001.0001b_00002 831 amiD | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MKALLWLVGLALLLTGCASEKGIIDKEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYNIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGISAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.0321.00001.0002b_00003 381 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPHFIAECTENIREQADLPGLFSKVNEALAASGIFPIGGIRSRAHWLDTWQMADGKHDYA
+FVHMTLKIGAGRSLESRQEVGEMLFGLIKAHFADLMENRYLALSFEIAELHPTLNYKQNN
+VHALFK
+>GENO.0321.00001.0002i_00004 1410 NA | hypothetical protein | NA | NA | NA
+MSMPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFAD
+GQTVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNV
+TLDVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQ
+MDGARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERINCTNGKINWGIGIGLAGSTY
+DNSYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPGFSKNAGIDNATI
+AIYGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQI
+SSGNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQ
+FMARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GENO.0321.00001.0002i_00005 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEG
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GENO.0321.00001.0002i_00006 735 trmD_1 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MFRAITDYGVTGRAVKKGLLNIQSWSPRDFAHDRHRTVDDRPYGGGPGMLMMVQPLRDAI
+HAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGVDERVIQTEIDEEW
+SIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFADGLLDCPHYTRPEVLEGME
+VPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQQQHKH
+DGMA
+>GENO.0321.00001.0002i_00007 828 trmD_2 | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MMGWHSRHMGSQRRRANAQYVFIGIVSLFPEMFRAITDYGVTGRAVKKGLLNIQSWSPRD
+FAHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVS
+ELATNQKLILVCGRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVL
+GHEASAIEDSFADGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRR
+PELLENLALTEEQARLLAEFKTEHAQQQHKHDGMA
+>GENO.0321.00001.0002i_00008 465 NA | hypothetical protein | NA | NA | NA
+MKFVAPEQAPEQAEVIKNTPFWPDVDLSEFRSVMRTDGTVTQPRLKQVVLTAISEVNAEL
+YDFRNRQQMLGWRTLAEVPAEMLDGKSERIRHYHNAVFCWARAVLNERYQDYDATASGVK
+RGEELAEASGDLWRDARWAISRVQDVPHCTVELI
+>GENO.0321.00001.0002i_00009 261 NA | hypothetical protein | NA | NA | NA
+MAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGILTRRYGLDKE
+MVMDFFKENHSGMAVRFFMAGYRLEG
+>GENO.0321.00001.0002i_00010 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLYYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GENO.0321.00001.0002b_00011 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
+FALLAVPFFVLSGVIMNSGGIAARLVNFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
+ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
+GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
+GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
+SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
+DPVHFGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
+IPEITLFLPRLLGIM
+>GENO.1216.00002.0001b_00001 831 amiD_1 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.1216.00002.0001i_00002 831 amiD_2 | N-acetylmuramoyl-L-alanine amidase AmiD | 3.5.1.28 | similar to AA sequence:UniProtKB:P75820 | COG:COG3023
+MRALLWLVGLALLLTGCASEKGIIDEEGYQLDTRHRAQAAYPRIKVLVIHYTAENFDVSL
+ATLTGRNVSSHYLIPATPPLYGGKPRIWQLVPEQDQAWHAGVSFWRGATRLNDTSIGIEL
+ENRGWRMSGGVKSFAPFESAQIQALIPLAKDIIARYDIKPQNVVAHADIAPQRKDDPGPR
+FPWRELAAQGIGAWPDAQRVAFYLAGRAPYTPVDTATVLALLSRYGYEVKADMTAREQQR
+VIMAFQMHFRPAQWNGIADAETQAIAEALLEKYGQD
+>GENO.1216.00002.0001i_00003 474 hpcD | 5-carboxymethyl-2-hydroxymuconate Delta-isomerase | 5.3.3.10 | similar to AA sequence:UniProtKB:Q05354 | NA
+MPKRRRLPKHYWRSTARINRARYREDSLFEDMPHFIAECTENIREQADLPGLFSKVNEAL
+AASGIFPIGGIRSRAHWLDTWQMADGKHDYAFVHMTLKIGAGRSLESRQEVGEMLFGLIK
+AHFADLMENRYLALSFEIAELHPTLNYKQNNVHALFK
+>GENO.1216.00002.0001i_00004 225 pspB | Phage shock protein B | NA | similar to AA sequence:UniProtKB:P0AFM9 | NA
+MSALFLAIPLTIFVLFVLPIWLWLHYSNRAGRGELSQSEQQRLLQLTDDAQRMRERIQAL
+EDILDAEHPNWRER
+>GENO.1216.00002.0001i_00005 1404 NA | hypothetical protein | NA | NA | NA
+MPATKFSRRTLLTAGSALAVLPFLRALPVQAREPRETVDIKDYPADDGIASFKQAFADGQ
+TVVVPPGWVCENINAAITIPAGKTLRVQGAVRGNGRGRFILQDGCQVVGEQGGSLHNVTL
+DVRGSDCVIKGVAMSGFGPVAQIFIGGKEPQVMRNLIIDDITVTHANYAILRQGFHNQMD
+GARITHSRFSDLQGDAIEWNVAIHDRDILISDHVIERIDCTNGKINWGIGIGLAGSTYDN
+SYPEDQAVKNFVVANITGSDCRQLVHVENGKHFVIRNVKAKNITPDFSKNAGIDNATIAI
+YGCDNFVIDNIDMTNSAGMLIGYGVVKGKYLSIPQNFKLNAIRLDNRQVAYKLRGIQISS
+GNTPSFVAITNVRMTRATLELHNQPQHLFLRNINVMQTSAIGPALKMHFDLRKDVRGQFM
+ARQDTLLSLANVHAINENGQSSVDIDRINHQTVNVEAVNFSLPKRGG
+>GENO.1216.00002.0001i_00006 774 hisP | Histidine transport ATP-binding protein HisP | NA | similar to AA sequence:UniProtKB:P02915 | COG:COG4598
+MSENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSED
+AIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV
+LGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPT
+SALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFVRHVSSHVIFLHQGKIEEEGDPEQVF
+GNPQSPRLQQFLKGSLK
+>GENO.1216.00002.0001i_00007 792 trmD | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | similar to AA sequence:UniProtKB:P0A873 | COG:COG0336
+MRAIYRRCVFIGIVSLFPEMFRAITDYGVTGRAVKNGLLNIQSWSPRDFTHDRHRTVDDR
+PYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVC
+GRYEGVDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVARFIPGVLGHEASAIEDSFA
+DGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEE
+QARLLAEFKTEHAQQQHKHDGMA
+>GENO.1216.00002.0001b_00008 288 NA | hypothetical protein | NA | NA | NA
+MNNHFGKGLMAGLHAPYAYSAHHAVNFCSEYKRGFVLGFTHRMFEKTGDRQLSAWEAGIL
+TRRYGLDKEMVMDFFKENHSGMAVRFFMAGYRLEG
+>GENO.1216.00002.0002b_00009 582 NA | hypothetical protein | NA | NA | NA
+MSTLLYLHGFNSSPRSAKACQLKNWLAERHPHVEMIVPQLPPYPADAAELLESLVLEHGG
+APLGLVGSSLGGYYATWLSQCFMLPAVVVNPAVRPFELLTDYLGQNENPYTGQQYVLESR
+HIYDLKVMQIDPLEAPDLIWLLQQTGDEVLDYRQAVAYYASCRQTVTEGGNHAFTGFEDY
+FNQIVDFLGLHSC
+>GENO.1216.00002.0002b_00010 1308 dctM | C4-dicarboxylate TRAP transporter large permease protein DctM | NA | similar to AA sequence:UniProtKB:O07838 | COG:COG1593
+MIDPIFASCTLIAVFVVLLAMGAPIGICIVIASFSTMMLVLPFDISMFATAQKMFSSLDS
+FALLAVPFFVLSGVIMNSGGIAARLINFAKLFTGKLPGSLSYTNIVGNMMFGAISGSAIA
+ASTSIGGVMVPMSAREGYDRGFAAAVNIASAPTGMLIPPTTAFILYALASGGTSIAALFA
+GGLVAGVLWGVGCMLVTLVVAKRRNYRVFFTVQKGMALKVAVEAIPSLLLIVIIVGGIVQ
+GIFTAIEASAIAVVYTLLLTMVFYRTLKIKDLPSILLQTVVMTGVIMFLLATSSAMSFSM
+SITNIPAALSDMILGISANKLVILLVITVFLLIIGAFMDIGPAILIFTPILLPIMAKLGV
+DPVHLGIIMIYNLAIGTITPPVGSGLYVGASVGKVKVEEVIKPLLPFYGAIIGVLLLITY
+IPEIILFLPRLLGIM
+>GENO.1216.00002.0003b_00011 255 NA | hypothetical protein | NA | NA | NA
+MIINGKLIKAKDLAKAAGVSRSTVIKYYGISRENYERVATERRKLAFELRASGLKWKEVA
+EKMNTTKYSAIAYYRRYLALEKNK
+>GENO.1216.00002.0003b_00012 780 NA | IS21 family transposase ISSen3 | NA | similar to AA sequence:ISfinder:ISSen3 | NA
+MVELQHQRLMVLAEQLQLDSLIGAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQA
+MYTRMAAFPAVKTFEEYDFTFATGAPQKQIQSLRSLSFIERNENIVLLGPSGVGKTHLAI
+AMGYEAVRAGIKVRFTTAADLLLQLSTSQRQGRYKTTLNRGVMAPKLLIIDEIGYLPFSQ
+EEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGE
+SYRLKQKRKAGVIAEANPE