Added tutorial for phylogenetic analysis

Author: SouradiptoC

Examples/Exome/phylo_input.fasta

@@ -0,0 +1,4 @@
+(
+CP045927.1:0.95728,
+FR821777.2:0.02340,
+CP000253.1:0.02380);

Examples/Exome/phylo_input_test.dnd

@@ -0,0 +1,137 @@
+>CP045927.1 partial exome of Staphylococcus agnetis
+ATGCCACAAAGTAAAAAAACCTCACCTAGAAGTACAAAAAAAGACAATCAAACTGAAGTA
+AATGAAACAAAAGAAAAAGACTCTGAAGAAGAGACGTCTAAAACTTCAACTTCAAAAAAG
+AAAAATACACGCGCTAGATCTCAATCTACTGCAACTAAGAAGAAAGCTGCATCCTCTAAA
+AAAGACGATGCAGCTTCTAAAGACAGTGAAAAAGTAGATGAGACAGAAGAAAAACCTAAG
+CGTAAATCAACGACACGTCGTCGTAGAACAACAAAAAAATCAGAAGATGATTCAACTAAA
+GATGAAAATAATGAAACAACTCATAAATCTACCAAGTCATCTCAAGCGACTACTAAGAAA
+AAAGATGATGAGGTAAAAGATGAAGAAGCAACCGAAGAAGCGTCTAAACAAGAAAAAGAA
+GACGACGCGGAGACTTCGGATTCAGAAACTGTTGATGACAAAGAAAAAGCGAACGATGCG
+GATGATAAAGAAGCATCTGACGCCCAAGACAAAGAAGAAGACACTGAGGATACAGAAGAA
+GAATCAGCTGAAGAAGAAGACTCTGAGGACTCAAAAGAAGAGGATGAAGAAGAAGCCTCC
+GAGGACTCAGAAGAAGAGGATGAAGAGGAAGCTTCCGAAACAGAGGAAGAAGAATCAGCT
+GAAGAAGATGAAGACTCTGAGGACTCAAAAGAAGAGGATGAAGAGGAAGCTTCCGAGGAC
+TCAAAAGAAGAAGAGGATGAAGAGGAAGCTTCCGAAACAGAGGAAGAAGAATCAGCTGAA
+GAAGAAGACTCCGAGGACTCAAAAGAGGAGGACGAAGAGGAAGCTTCCGAAACAGAGGAA
+AAAGAATCAGCTGAAGAAGAAGACTCCGAGGACTCAAAAGAGGAGGACGAAGAGGAAGCT
+TCCGAAACAGAGGAAAAAGAATCAGCTGAAGAAGAAGACTCCGAGGACTCAAAAGAAGAA
+GAGGATGAAGAGGAAGATTCAGAAACAGAGGAAGAAGAATCAACTGAAGAAGATGAAGAC
+TCTGAAGATACGGAAGATGATGAGGAAGAAGAAAAACAAGACACTGCATTATCTGTTAAA
+GAGCCGAAAAAAGGTTTTTGGGATAAACTGACGAAAAACAAAAAATCAGTGAAAATCAAG
+AAAAATGAGGTTTCTAAAGAAGCTAAAGGCATTCAAACTAAAATAGAAATCAATGATGAT
+ACGGTTTCTAAAAAATAAATGAAGCAAAAGGAGAAGGAAAAGATAATTAAGAAAACGATT
+GTTGGTGGCATATTAGGTGCTACAATGGGCTATTTATCTACGTCCAAAAGTAATCCGAAA
+TCAGGAACGATGACGAAAGATCGGTTAGACCATATGAAATCTTTAACGTCACAACTTTTA
+AACCAACAATCTCAATCTAAAAAGTCTAAATCCTCAGTATTTAGTTCATTTACTAAAAAC
+AAAGCGACAAAGCGGAAAGGATCTTTATGGGATAAATTCAAAAAAGATCACAAGGGCGAT
+AGAAAGGACAAGAAGTCTATGAAAAAAACGAAAATTAATTCACGTATTTTTCATAATGAT
+GATACGTCAACGAAAGACTCAGATAACAAGGGAAATGTATTAAACAGTTTGAAAAAAGAT
+AAGAAAGAGAAAACACAATCAGCGTCTAAAACGCCGCGCACAGATGCGAAAAAGGCAAAA
+GCAAAAGTGAAAGAAGAGGGATCTAATCATGAGAAAAAGAACAAAGGGAAAACTATTTTC
+AAAAAGTCCGAGAAAAGTGAAAAAAATGGTGATCAAACAAAAAATGAAAAAGCTCGCAAA
+AAAGATGCGAAAAAAGCTGAAAAGAATGGAAAAGAAGCTAAAATAACAAAGGAAAAAGAG
+AAACCTTCTTTGTTGGACCGTTTTAAAAGAGATGATCAATCATCTAAAAAAACGAATAAG
+AAAAAAGAGAAATCAAACAAAGATGACTCTTTAAAAGATTCAATTTTGAATAAGTTTGGT
+AAAAATGGTGCGAACAAAAAGAAGGATTTAAAAAAAAAGAAGAAGAAGCAGAAAGAGAAA
+AAGGGGCTTCTCGGGAAAATGAGGAAGTGAATGGCAAATGACCCAAATTTACCACAAAAT
+GGATCAAGTAACTTAGTGGAAGTACTTGAGAAAGTACTTGATAAAGGTGTCGTAATCGCA
+GGTGACATTCGTGTTGGAATTGCTGATGTCGAGCTCCTTTCCATTAAAATACGTCTAATT
+GTGGCTTCAGTAGATAAAGCGAAAGAAATTGGTTTAGATTGGTGGGAAACAGATCCATAT
+CTCACTTCAAGAGCGACTGAAAATAAAATGAATCAACAAAAAGATTTAGAATCCGAAAAT
+CAAGAATTGTTGAATAAAATTGAAGCACTCGAAAGTAAAATTAATGCGAATGAGTTAAGT
+CAAGACACTAAGGTAGAAGAACCAGCGACAGCAAAGAATGGGGGACAAAAAGATGAAGCA
+AAAGGAGAAGGAAAAGATAATTAA
+>FR821777.2 partial exome of Staphylococcus argenteus
+ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCT
+GTAAGTTACTCAACTTTCCTAAAAGATACCGAGCTTTACACGATTAAAGATGGTGAAGCT
+ATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATT
+ATCCAAGCAATCTTATTTGATGTTGTAGGTTATGAAGTGAAACCTCATTTTATTACTACT
+GAGGAATTAGCAAATTATAGTAATAAAGATGTTTCTACGGTACAGGAAACACCAAAATCT
+TCTACTGAAACAACTGAAGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAAC
+ACATTTGACACATTTGTAATCGGACCTGGTAACCGCTTCCCACATGCAGCAAGTTTAGCC
+GTTGCCGAAGCACCAGCAAAAGCGTATAATCCATTATTTATATATGGAGGTGTTGGTTTA
+GGAAAAACCCATTTAATGCATGCCATTGGTCATCATGTTTTAGATAATAATCCAGATGCC
+AAAGTGATTTACACATCAAGTGAAAAATTCACAAACGAATTTATCAAATCGATTCGTGAT
+AACGAGGGTGAAGCTTTCAGAGAAAGATATCGTAATATCGACGTCTTATTAATCGATGAT
+ATTCAGTTCATACAAAATAAAGTTCAAACGCAAGAAGAATTTTTCTATACTTTTAATGAA
+TTACATCAGAATAACAAGCAAATCGTTATTTCGAGTGATCGACCACCAAAAGAGATTGCA
+CAATTAGAAGATCGATTACGTTCACGCTTTGAATGGGGGCTAATTGTTGATATTACGCCA
+CCAGATTACGAAACTCGAATGGCAATTTTGCAGAAGAAAATTGAAGAAGAGAAATTAGAT
+ATTCCACCAGAAGCTTTAAATTATATAGCAAATCAAATTCAATCTAATATTCGTGAATTA
+GAAGGTGCATTGACACGCTTACTTGCATATTCACAATTATTAGGAAAACCAATTACAACT
+GAATTAACTGCTGAAGCTTTAAAAGATATCATTCAAGCACCAAAATCTAAGAAAATTACA
+ATTCAAGATATTCAAAAGGTAGTAGGTCAGTACTATAATGTTAGAATTGAAGATTTCAGT
+GCTAAAAAACGTACAAAGTCAATCGCATATCCGCGTCAAATAGCTATGTACTTATCTAGA
+GAGCTTACTGATTTTTCATTACCTAAAATTGGTGAAGAATTTGGCGGGCGTGATCACACA
+ACTGTAATCCATGCTCATGAAAAGATATCTAAAGATTTAAAAGAAGATCCTATTTTTAAA
+CAAGAAGTAGAGAATCTTGAAAAAGAAATAAGAAATATTTAAATGATGGAATTCACTATT
+AAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCAATATCACCAAGAACA
+ACATTACCAATTTTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTGATACTAACT
+GGTTCAGACTCTGAAATTTCAATTGAAATCACTATTCCTAAAACTGTTGATGGCGAAGAT
+ATTGTCAACATTTCAGAAACAGGTTCAGTTGTGTTACCTGGACGATTCTTTGTTGATATT
+ATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAGCAATTCCAAACATTA
+ATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTA
+TTACCACAAGTTTCTAGAGATGACGCAATTCAATTGTCAGTAAAAGTGCTTAAAAACGTG
+ATTGCACAAACGAATTTCGCAGTGTCCACCTCAGAAACACGCCCAGTATTGACTGGTGTG
+AACTGGCTTATACAAGAAAATGAATTAATATGCACAGCGACTGACTCACACCGCTTGGCT
+GTAAGAAAGTTGCAGTTAGAAGATGTTTCTGAAAATAAAAATGTCATCATTCCAGGTAAA
+GCCTTAGCTGAACTAAATAAAATTATGTCTGATAGTGAAGAAGACATTGATATCTTCTTT
+GCTTCAAATCAAGTTTTATTCAAAGTAGGAAATGTAAACTTTATTTCTCGATTATTAGAG
+GGACATTATCCTGATACAACACGTTTATTCCCTGAAAACTATGAAATTAAATTAAGTATA
+GACAATGGCGAATTTTATCATGCAATTGATCGTGCATCTTTATTAGCACGTGAAGGTGGC
+AATAACGTTATTAAATTAAGTACAGGTGATGACGTTGTTGAATTGTCTTCTACATCACCA
+GAAATTGGTACTGTTAAAGAAGAAGTTGATGCAAATGATGTTGAAGGCGGAAACTTAAAA
+ATTTCTTTCAACTCTAAATATATGATGGACGCTTTAAAAGCAATTGATAATGACGAAGTT
+GAGGTTGAATTCTTTGGTACAATGAAGCCGTTCATTTTAAAACCAAAAGGTGACGACTCA
+GTAACGCAATTAATTTTACCAATCAGAACATACTAATTGGTTCAAGAAGTTGTAGTAGAA
+GGCGACATCAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAGTCTGGTGGTCAA
+GCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACACGTCGC
+GGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAGTTACCTGAAGATGCTGGT
+TCTTTCTTAATCATTCATCAAGGTGAACAATGA
+>CP000253.1 partial exome of Staphylococcus aureus
+ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCT
+GTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCT
+ATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATT
+ATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTTAAACCTCACTTTATTACTACT
+GAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAACAACAAAACCT
+TCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAAC
+ACATTTGACACTTTTGTAATCGGACCCGGTAACCGCTTTCCACATGCAGCGAGTTTAGCT
+GTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTTATCTATGGAGGTGTTGGTTTA
+GGAAAAACCCATTTAATGCATGCCATTGGTCATCATGTTTTAGATAATAATCCAGATGCC
+AAAGTGATTTACACATCAAGTGAAAAATTCACAAATGAATTTATTAAATCAATTCGTGAT
+AACGAAGGTGAAGCTTTCAGAGAAAGATATCGTAATATCGACGTCTTATTAATCGATGAT
+ATTCAGTTCATACAAAACAAGGTACAAACACAAGAAGAATTTTTCTATACTTTTAATGAA
+TTGCATCAGAATAACAAGCAAATAGTTATTTCGAGTGATCGACCACCAAAGGAAATTGCA
+CAATTAGAAGACCGATTACGTTCACGCTTTGAATGGGGGCTAATTGTTGATATTACGCCA
+CCAGATTATGAAACTCGAATGGCAATTTTGCAGAAGAAAATTGAAGAAGAAAAATTAGAT
+ATTCCACCAGAAGCTTTAAATTATATAGCAAATCAAATTCAATCTAATATTCGTGAATTA
+GAAGGTGCATTAACACGTTTACTTGCATATTCACAATTATTAGGAAAACCAATTACAACT
+GAATTAACTGCTGAAGCTTTAAAAGATATCATTCAAGCACCAAAATCTAAAAAGATTACC
+ATCCAAGATATTCAAAAAATTGTAGGCCAGTACTATAATGTTAGAATTGAAGATTTCAGT
+GCAAAAAAACGTACAAAGTCAATTGCATATCCGCGTCAAATAGCTATGTACTTGTCTAGA
+GAGCTTACAGATTTCTCATTACCTAAAATTGGTGAAGAATTTGGTGGGCGTGATCATACG
+ACCGTCATTCATGCTCATGAAAAAATATCTAAAGATTTAAAAGAAGATCCTATTTTTAAA
+CAAGAAGTAGAGAATCTTGAAAAAGAAATAAGAAATGTATAAATGATGGAATTCACTATT
+AAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCTATTTCACCAAGAACA
+ACATTACCTATATTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTTATATTAACT
+GGTTCAGACTCTGAAATTTCAATAGAAATCACTATTCCTAAAACTGTAGATGGCGAAGAT
+ATTGTCAATATTTCAGAAACAGGCTCAGTAGTACTTCCTGGACGATTCTTTGTTGATATT
+ATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAACAATTCCAGACATTA
+ATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTA
+TTACCTCAAGTTTCTAGAGATGACGCAATTCAATTGTCGGTAAAAGTGCTTAAAAACGTG
+ATTGCACAAACAAATTTTGCAGTGTCCACCTCAGAAACACGCCCAGTACTAACTGGTGTG
+AACTGGCTTATACAAGAAAATGAATTAATATGCACAGCGACTGACTCACACCGCTTGGCT
+GTAAGAAAGTTGCAGTTAGAAGATGTTTCTGAAAACAAAAATGTCATCATTCCAGGTAAG
+GCTTTAGCTGAATTAAATAAAATTATGTCTGACAATGAAGAAGACATTGATATCTTCTTT
+GCTTCAAACCAAGTTTTATTTAAAGTTGGAAATGTGAACTTTATTTCTCGATTATTAGAA
+GGACATTATCCTGATACAACACGTTTATTCCCTGAAAACTATGAAATTAAATTAAGTATA
+GACAATGGGGAGTTTTATCATGCGATTGATCGTGCCTCTTTATTAGCGCGTGAAGGTGGT
+AATAACGTTATTAAATTAAGTACAGGTGATGACGTTGTTGAATTGTCTTCTACATCACCA
+GAAATTGGTACTGTAAAAGAAGAAGTTGATGCAAACGATGTTGAAGGTGGTAGCCTGAAA
+ATTTCATTCAACTCTAAATATATGATGGATGCTTTAAAAGCAATCGATAATGATGAGGTT
+GAAGTTGAATTCTTCGGTACAATGAAACCATTTATTCTAAAACCAAAAGGTGACGACTCG
+GTAACGCAATTAATTTTACCAATCAGAACTTACTAAGTGATTATTTTGGTTCAAGAAGTT
+GTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCT
+GGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAA
+ACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAA
+GATGCTGGTTCTTTCTTAATCATTCATCAAGGTGAACAATGA

Examples/Exome/phylo_input_test.fasta

@@ -0,0 +1,147 @@
+>CP045927.1 partial exome of Staphylococcus agnetis
+-----------------ATGCCACAAAGTAAAAAAA----------------CCTCACCT
+AGAAGTACAAAAAAAGA---CAATCAAACTGAAGTAAATGAAACAAAAGAAAAAGACTCT
+GAAGAAGAGACGTCTAAAACTTCAACTTCAAAAAAGAAAAATACA---------------
+-----CGCGCTAGATCTCAATCTACT-GCAACTAAGAAGAAAGCTGCATCCTCTAAAAAA
+GACGATGCAGCTTCTAAAGACAGTGAAAAAGTAGATGAGACAGAAGAAAAACCTAAGCGT
+AAATCAACGACACGTCGTCGTAGAACAACAAAAAAATCAGAAGATGATTCAACTAAAGAT
+GAAAAT------AATGAAACAACTCATAAATCTACCAAGTCATCTCAAGCGACTACTAAG
+AAAAAAGATGATGAGGTAAAAGATGAAGAAGCAACCGAAGAAGCGTCTAAACAAGAAAAA
+GAAGACGACGCGGA-GACTTCGGA--------TTCAG---AAACTGTTGATGACAAAGAA
+AAAGCGAACGATGCGGATGATAAAGA------AGCATCTGACGCCCAAGACAAAGAAGAA
+GACACTGAGGATACAGAAGAAGAATCAGCTGAAGAAGAAGACTCTGAGGACTCAAAAGAA
+GAGGATG-AAGAAGAAGCCTCCGAGGACTCAGA----AGAAGAGGA--------------
+-----TGAAGAGGAAGCTTCCGAAACAGAGG-----------AAGAAGAATCAGCTGAAG
+AAGATGAAGACTCTGAGGACTCAAAAG-AAGA----GGATGAAGAGGAAGCTTCCGAGGA
+CTCAAAAGAAGAAGAGGATGAAGAGGAAGCTTCCGAAACAGAGGAAGAAGAATCAGCTGA
+AGAAGAAGACTCCGAGGACTCAAAAGAGGAGGACGAAGAGGAAGCTTCCGAAACAGAGGA
+AAAAGAATCAGCTGAAGAAGAAGACT-------CCGAGGACTCAAAAGAGGAGGACG---
+--AAGAGGAAGCTTCCGAAACA-GAGGAA-----------AAAGAATCAGCTGAAGA---
+------AGAAGACTCCGAGGACTCAAAAGAAGAAGAGGATGAAGAGGAAGATTCAGAAAC
+AGAGGAAGAAGAATCAACTGAAGAAGATGAAGACTCTGAAGATACGGAAGATGATGAGGA
+AGAAGAAAA-----ACAAGACACTGCATTATCTGTT--AAAGAGCCGAAAAAAGGTTTTT
+GGGATAAACTGAC---GAAAAACAAAAAATCAGTGAAAATCAAGAAAAATGAGGTTTCTA
+AAGAAGCTAAAGGCATTCAAACTAAAA------------TAGAAATCAATGATGATACGG
+TTTCTAAAAAATAAATGAAGCAAAAGGAGAAGGAAAAGA---------------------
+---TAATTAAGAAAACGATTGTTGGTGGCATATTAGGTGCTACAATGGGCTATTTATCTA
+CGTCCAAAAGTAATCCGAAATCAGGAACGATGACGAAAGATCGGTTAGACCA--------
+TATGAAAT-CTTTAACGTCACAACTTTTAAACCAACAATCTCAATCTAAAAAGTCTAAAT
+CCTCAGTATTTAGTTCATTTACTAAAAACAAAGCG-----ACAAAGCGGAAAGGATCTTT
+ATGGGATAAATTCAAAAAAGATCACAAGGGCGATAGAAAGGACAAGAAGTCTATGAAAAA
+-----AACGAAAATTAATTCACGTATTTTTCATAATGA--------TGATACGTCAACGA
+AAGACTCAGATAACAAGGGAAATG--------------TATTAAACAGTTTGAA--AAAA
+GATAAGAAAGAGAAAACACAATCAGCGTCTAAAACGCCGCGCACAGATGCGAAAAAGGCA
+AAAGCAAAAGTGAAA-GAAGAGGGATC------------TAATCATGAGAAAAAGAACAA
+AGGGAAAACTATTTTCAAAAAGTCCGAGAAAAGTGAAAAAAATGGTGATCAAACAAAAAA
+TGAAAAAGCTCGCAAAAAAGATGCGAAAAAAGCTGAAAAGAATGGAAAAGAAGCTAAAAT
+AACAAAGGAAAAAGAGAAACCTTCTTTGTTGGA----CCGTTTTAAAAGAGATGATC--A
+ATCATCTAAAAA-AACGAATAA------GAAAAAAGAGAAATCAAACAAAGATGACTCTT
+TAAAAGATTCAATTTTGAATAAGTTTGGTAAAAATGGTGCGAACAAAAAGAAGGATTTAA
+AAAAAAAGAAGAAGAAGCAGAAAGAGAAAAAGGGGCTTCTCGGGAAAAT----GAGGAAG
+TGAATGGCAAATGACCCAAATTTACCACAAAATGGATCAAGTAACTTAGTGGAAGTACTT
+GAGAAAGTACTTGATAAAGGTGTCGTAA------TCGCAGGTGACATTCGTGTTGGAATT
+GCTGATGTCGAGCTCCTTTCCATTAAAATACGTCTAATTGTGGCTTCAGTAGATAAAGCG
+AA---AGAAATTGGTTTAGATTGGTGGGAAACAGATCCATATCTCACTTCAAGAGCGACT
+GAAAATAAAATGAATCAACAAAAAGATTTAGAATCCGAAAATCAAGAATTGTTGAATAAA
+ATTGAAG------CACTCGAAAGTAAAATTAA----------------------------
+--------------------TGCGAATGAGTTAAGTCAAGACACTAAGGTAGAAGAA---
+------------CCAGCGACAGCAAAGAATGGGGGACAAAA---------AGATGAAGCA
+AAAGGAGAAGGAAAAGATAATTAA------------------------------
+>FR821777.2 partial exome of Staphylococcus argenteus
+ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCT
+GTAAGTTACTCAACTTTCCTAAAAGATACCGAGCTTTACACGATTAAAGATGGTGAAGCT
+ATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATT
+ATCCAAGCAATCTTATTTGATGTTGTAGGTTATGAAGTGAAACCTCATTTTATTACTACT
+GAGGAATTAGCAAATTATAGTAATAAAGATGTTTCTACGGTACAGGAAA-----------
+----CACCAAAATCTTCTACTGAAACAACTGAAGA---TAATCATGTGCTTGGTAGAGAG
+CAATTCAATGCCCATAACACATTTGACACATTTG--TAATCGGACCTGGTAACCGCTTCC
+C-ACATGCAGCAAGTTTAGCCGTTGCCGAAGCACCAGCAAAAGCGTATAATCCATTATTT
+ATATATGGAGGTGTTGGTTTAGGAAAAACCCATTTAATGCATGCCATTGGTCATCATGTT
+TTAGATAATAATCCAGATGCCAAAGTGATTTACACATCAAGTGAAAAATTCACAAACGAA
+T---------TTAT------CAAATCGATTCGTGATAACGAGGGTGAAGCTTTCAGAGAA
+AGATATCGTAATATCGACGTCTTATTAATCGATGATATTCAGTTCATACAAAATAAAGTT
+CAAACGCAAGAAGAATTTTTCTATACTTTTAATGAATTACATCAGAATAACAAGCAAATC
+GTTATTTCGAGTGATCGACCACCAAAAGAGATTGCACAATTAGAAGATCGATTACGTTCA
+CGCTTTGAA--TGGGGGCTAATTGTTGATATTACGCCACCAGATTACGAAACTCGAAT--
+---GGCAATTTTGCAGAAGAAAATTGAAGAAGAGAAATTAGATATTCCACCAGAAGCTTT
+AAATTATATAGCAAATCAAATTCAATCTAATATTCGTGAATTAGAAGGTGCATTGACACG
+CTTACTTGCATATTCACAATTATTAGGAAAACCAATTACAACTGAATTAACTGCTGAAGC
+TTTAAAAGATATCATTCAAGCACCAAAATCTAAGAAAATTACAATTCAAGATATTCAAAA
+G------------------GTAGTAGGTCAGTACTATAATGTTAGAATTGAAGATTTCAG
+TGCTAAAAAACGTACAAAGTCAATCGCATATCCGCGTCAAATAGCTATGTACTTATCTAG
+AGAGCTTACTGATTTTTCATTACCTAAAATTGGTGAAGAATTT-------GGCGGGCGTG
+ATCACACAACTGTAATCCATGCTCATGAAAAGATATCTAAAGATTTAAAAGAAGATCCTA
+TTTTTAAACAAGAAGTAGAGAATCTTGAAAAAGAAATAAGAAATATTTAAATGATGGAAT
+TCACTATTAAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCAATATCAC
+CAAGAACAACATTACCAATTTTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTGA
+TACTAACTGGTTCAGACTCTGAAATTTCAATTGAAATCACT-ATTCCTAAAACTGTTGAT
+GGCGAAGATATTGTCAACATTTCAGAAACAGGTTCAGTTGTGTTACCTGGACGATTCTTT
+GTTG---ATATTATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAGCAA
+TTCCAAACATTAATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGAT
+CAATATCCTTTATTACCACAAGTTTCTAGAGATGACGCAATTCAATTGTCAGTAAAAGTG
+CTTAAAAACGTGATTGCACAAACGAATTTCGCAGTGTCCA-----CCTCAGAAACACGCC
+CAGTATTGACTGGTGTGAACTGGCTTATACAAGAAAATGAATTAATATGCACAGCGACTG
+ACTCACACCGCTTGGCTGTAAGAAAGTTGCAG--TTAGAAGATGTTTCTGAAAATAAAAA
+TGTCATC------ATTCCAGGTAAAGCCTTAGCTGAACTAAATAAAATTATG--TCTGAT
+AGTGAAGAAGACATTGATATCTTCTTTGCTTCAAATCAAGTTTTATTCAAAGTAGGAAAT
+GTAAACTTTATTTCTCGATTATTAGAGGGACATTATCCTGATACAACACGTTTATTCCCT
+GAAAACTATGAAATTAAATTAAGTATAGAC------------------------------
+-------------AATGGCGAATTTTATCATGCAATTGATCGTGCATCTTTATTAGCACG
+TGAAGGTGGCAATAACGTTATTAAA--TTAAGTACAGGTGATGACGTTGTTGAATTGTCT
+TCTACATCACCAGAAATTGGTACTGTTAAAGAAGAAGTTGATGCAAATGATGTTGAAGGC
+GGAAACTTAAAAATTTCTTTCAACTCTAAATATATGATGGACGCTTTAAAAGCAATTGAT
+AATGACGAAGTTGAGGTTGAATTCTTTGGTACAATGAAGCCGTTCATTTTAAAACCAAAA
+GGTGACGACTCAGTAACGCAATTAATTTTACCAATCAGAACATACTAATT---------G
+GTTCAAGAAGTTGTAGTAGAAGGCGACATCAATTTAGGTCAATTTCTAAAAACAGAAGGG
+ATTATTGAGTCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAAT
+GGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCA
+GAGTTACCTGAAGATGCTGGTTCTTTCTTAATCATTCATCAAGGTGAACAATGA
+>CP000253.1 partial exome of Staphylococcus aureus
+ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCT
+GTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCT
+ATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATT
+ATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTTAAACCTCACTTTATTACTACT
+GAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAA-----------
+----CAACAAAACCTTCTACTGAAACAACTGAGGA---TAATCATGTGCTTGGTAGAGAG
+CAATTCAATGCCCATAACACATTTGACACTTTTG--TAATCGGACCCGGTAACCGCTTTC
+C-ACATGCAGCGAGTTTAGCTGTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTT
+ATCTATGGAGGTGTTGGTTTAGGAAAAACCCATTTAATGCATGCCATTGGTCATCATGTT
+TTAGATAATAATCCAGATGCCAAAGTGATTTACACATCAAGTGAAAAATTCACAAATGAA
+T---------TTAT------TAAATCAATTCGTGATAACGAAGGTGAAGCTTTCAGAGAA
+AGATATCGTAATATCGACGTCTTATTAATCGATGATATTCAGTTCATACAAAACAAGGTA
+CAAACACAAGAAGAATTTTTCTATACTTTTAATGAATTGCATCAGAATAACAAGCAAATA
+GTTATTTCGAGTGATCGACCACCAAAGGAAATTGCACAATTAGAAGACCGATTACGTTCA
+CGCTTTGAA--TGGGGGCTAATTGTTGATATTACGCCACCAGATTATGAAACTCGAAT--
+---GGCAATTTTGCAGAAGAAAATTGAAGAAGAAAAATTAGATATTCCACCAGAAGCTTT
+AAATTATATAGCAAATCAAATTCAATCTAATATTCGTGAATTAGAAGGTGCATTAACACG
+TTTACTTGCATATTCACAATTATTAGGAAAACCAATTACAACTGAATTAACTGCTGAAGC
+TTTAAAAGATATCATTCAAGCACCAAAATCTAAAAAGATTACCATCCAAGATATTCAAAA
+A------------------ATTGTAGGCCAGTACTATAATGTTAGAATTGAAGATTTCAG
+TGCAAAAAAACGTACAAAGTCAATTGCATATCCGCGTCAAATAGCTATGTACTTGTCTAG
+AGAGCTTACAGATTTCTCATTACCTAAAATTGGTGAAGAATTT-------GGTGGGCGTG
+ATCATACGACCGTCATTCATGCTCATGAAAAAATATCTAAAGATTTAAAAGAAGATCCTA
+TTTTTAAACAAGAAGTAGAGAATCTTGAAAAAGAAATAAGAAATGTATAAATGATGGAAT
+TCACTATTAAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCTATTTCAC
+CAAGAACAACATTACCTATATTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTTA
+TATTAACTGGTTCAGACTCTGAAATTTCAATAGAAATCACT-ATTCCTAAAACTGTAGAT
+GGCGAAGATATTGTCAATATTTCAGAAACAGGCTCAGTAGTACTTCCTGGACGATTCTTT
+GTTG---ATATTATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAACAA
+TTCCAGACATTAATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGAT
+CAATATCCTTTATTACCTCAAGTTTCTAGAGATGACGCAATTCAATTGTCGGTAAAAGTG
+CTTAAAAACGTGATTGCACAAACAAATTTTGCAGTGTCCA-----CCTCAGAAACACGCC
+CAGTACTAACTGGTGTGAACTGGCTTATACAAGAAAATGAATTAATATGCACAGCGACTG
+ACTCACACCGCTTGGCTGTAAGAAAGTTGCAG--TTAGAAGATGTTTCTGAAAACAAAAA
+TGTCATC------ATTCCAGGTAAGGCTTTAGCTGAATTAAATAAAATTATG--TCTGAC
+AATGAAGAAGACATTGATATCTTCTTTGCTTCAAACCAAGTTTTATTTAAAGTTGGAAAT
+GTGAACTTTATTTCTCGATTATTAGAAGGACATTATCCTGATACAACACGTTTATTCCCT
+GAAAACTATGAAATTAAATTAAGTATAGAC------------------------------
+-------------AATGGGGAGTTTTATCATGCGATTGATCGTGCCTCTTTATTAGCGCG
+TGAAGGTGGTAATAACGTTATTAAA--TTAAGTACAGGTGATGACGTTGTTGAATTGTCT
+TCTACATCACCAGAAATTGGTACTGTAAAAGAAGAAGTTGATGCAAACGATGTTGAAGGT
+GGTAGCCTGAAAATTTCATTCAACTCTAAATATATGATGGATGCTTTAAAAGCAATCGAT
+AATGATGAGGTTGAAGTTGAATTCTTCGGTACAATGAAACCATTTATTCTAAAACCAAAA
+GGTGACGACTCGGTAACGCAATTAATTTTACCAATCAGAACTTACTAAGTGATTATTTTG
+GTTCAAGAAGTTGTAGTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGG
+ATTATTGAATCTGGTGGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAAT
+GGAGTGCGTGAAACACGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCA
+GAATTACCTGAAGATGCTGGTTCTTTCTTAATCATTCATCAAGGTGAACAATGA