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commit 4908224456491b258e1658a99738a494fdb4bd34 Author: Canberk Koç <canberk...@gmail.com> Date: Wed Oct 12 23:56:53 2016 +0300 Autopkgtest fixed --- debian/changelog | 6 +- debian/phyml-examples/example.nex | 472 ++++++++++++++++++++++++++++++++++++++ debian/phyml.examples | 1 + debian/tests/run-unit-test | 2 +- 4 files changed, 478 insertions(+), 3 deletions(-) diff --git a/debian/changelog b/debian/changelog index d3487d7..a99ee86 100644 --- a/debian/changelog +++ b/debian/changelog @@ -4,7 +4,7 @@ phyml (3:3.2.0+dfsg-3) UNRELEASED; urgency=medium [ Canberk Koç ] * autopkgtest added - + * fix autopkgtest [ Andreas Tille ] * Add missing Depends: openmpi-bin * use wrapper to select MPI version if applicable @@ -12,7 +12,9 @@ phyml (3:3.2.0+dfsg-3) UNRELEASED; urgency=medium * Fix missing declaration * hardening=+all,-pie - -- Canberk Koç <canberk...@gmail.com> Wed, 20 Jul 2016 03:01:14 +0300 + + + -- Canberk Koç <canberk...@gmail.com> Wed, 12 Oct 2016 23:51:39 +0300 phyml (3:3.2.0+dfsg-2) unstable; urgency=medium diff --git a/debian/phyml-examples/example.nex b/debian/phyml-examples/example.nex new file mode 100644 index 0000000..38f367b --- /dev/null +++ b/debian/phyml-examples/example.nex @@ -0,0 +1,472 @@ +#NEXUS +BEGIN DATA; +DIMENSIONS NTAX=7 NCHAR=2888; +FORMAT DATATYPE=DNA; + +MATRIX + +ENSG00000048405 -------------------------------------------------- +ENSMUSG00000039841 -------------------------------------------------- +ENSDARG00000004594 GTCCTTAATTTCCTTAGTTTGATGCACACGTTGTGGGGGTCAGATGTAAA +ENSDARG00000039843 -------------------------------------------------- +ENSGACG00000018833 -------------------------------------------------- +ENSORLG00000013219 -------------------------------------------------- +ENSTNIG00000018490 -------------------------------------------------- + +-------------------------------------------------- +-------------------------------------------------- +TCACCAATCTGGCGACAACATCGGGTGCCACATTTTGGTGGTCTCAAACA +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- + +-------------------------------------------------- +-------------------------------------------------- +TCCATTGCACCTTTGCGCAACAGCCGCTTCTCCGCCGAGAGGTCCTCGCG +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- + +-------------------------------------------------- +-------------------------------------------------- +GTGCACAAAGGCAGCTTCCGAGAGGGCAGCGTCAGCGCGGAGGCGAGAGA +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- + +-------------------------------------------------- +-------------------------------------------------- +AACAATCTCCAGATCGCCTTCTACCATCTTTACTCGAAAGCGAACGTTGT +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- + +-----------------------AT-------GCC---TTTAAGG----- +-----------------------AT-------GCC---TTTGAGG----- +TTTTACACGAGCCTTTTAGGTTCATAAAAGGGGCC---TCTGAGATGGAG +-----------------------ATGGAGGAAGCTCCGTCCAATG----- +-------------------------------------------------- +-------------------------------------------------- +-------------------------------------------------- + +------------------------------------GACAAATACTGTCA +------------------------------------GACAAATACTGTCA +GCTACTAAGAGTGAAGTTCAGGGAAGCCTGACTAGTGACAAATACTGCCA +-------------------------------------AAAAATCTTGCCA +---------------------------------AAAAATGAATATTGCAA +-------------------------------------------------- +-------------------------------------------------- + +GACTGA------------CCACCATCATCA-----CGGA----------- +AACGGA------------CCACCATCATCA-----CGGA----------- +GACTGAGACACTTCAGGCCTGCTGTTGCCAAACAACAGAAACCCCTCAAG +GACGGA-------------TGTCTCTCCTGGAT--CTGA----------- +ATCATA------------TCGCAAATGCAG-------------------- +-------------------------------------------------- +-------------------------------------------------- + +-----TGCTGTGAA----CCAGTTTATATCCTGGAACCTGGAGATCCTCC +-----TGCTGCGAA----CCAGTTTATATCCTGGAGCCTGGAGATCCTCC +AGCCTTGTGGCAAAAAT-CCAGTGCATCTGATTGAGCCTGGTGATCCACC +--TCATCCCATCAAGACACCAGTTTACTCAACAGAACCAGGAGATCCTCC +-------CAGTGAA-------AGTTTCTGTGTGGAGCCTGGAGATCCTCC +---------------------------------GAGCCTGGTGATCCTCC +------------------------------GTGGAACCTGGAGACCCTCC + +TTTGTTACAGCAACCACTACAGACATCCAAATCTGGTATTCAACAAATAA +CTTGTTACAGCAACCAGTGCAGACATCCAAATCTGGTATTCAGCAAATAA +CCTGCTTCAACAACAGCTTCAGACATCCAAGTCAGGAATTCATCAAATTA +CTTACTCCAAACCCCAATGCTCACCTCTAAATCTGGCATCCAGCAGATCA +CCTGCTCCAGCAGCCTCTGCAGACCTCCAAATCCGGGATCCAGCAGATAA +TCTTCTTCAGCAGCCTCTGCAGACCTCCAAGTCAGGGATTCAGCAGATCA +CCTGCTTCAGCAGCCTCTGCAGACCTCCAAATCTGGGATCCAGCAGATCA + +TTGAGTGCTTTCGATCAGGAACTAAACAACTTAAGCATATTTTATTAAAA +TTGAGTGCTTTCGATCAGGAACCAAACAACTTAAACATATTTTATTAAAA +TTGAGTGTTTTCGCTCAGGTACAGCTCAACTAAAACAAATGCTGTTGAAG +TTGAGTGTTTCCGCACAGGTACTGCACAGCTGAAGCACATTCTCCTGAAA +TCGAATGCTTCCGCTCAGGCACCAGCCAGCTGAAACACATGCTGCTGAGG +TTGAATGCTTCAGATCAGGCACCAGCCAGCTGAAGCACATCCTGTTACAG +TCGAGTGCTTCCGCTCAGGAACAGCTCAGCTCAAACACATGCTGCTGAGG + +GATGTGGACACTATTTTTGAATGTAAGTTATGCCGCAGTCTCTTCAGAGG +GATGTGGACACTATTTTTGAATGTAAATTATGCCGTAGTCTCTTTAGAGG +GAAGTTGACACCATATTTGAATGTAAAATCTGTCGAAGTCTGTTTCGTGG +GAGGTGGACACCATCTTTGAATGTAAACTCTGCCGCAGTCTCTTCCGTGG +GAGGTGGACACCATCTTTGAGTGCAAACTGTGTCGCAGTCTGTTCAGAGG +GAGGTGGACACCATCTTTGAGTGTAAAATTTGCCGCAGCCTTTTCAGGGG +GAGGTGGACACCATCTTTGAATGTAAGCTGTGCAGGAGTCTGTTCAGAGG + +ATTACCAAATTTAATTACCCATAAAAAATTCTACTGC-----CCAC-CAA +ATTACCAAATTTAATTACCCATAAAAAATTTTACTGC-----CCAC-CAA +TCTACCAAATCTGGTCACACACAAGGAGCTTTACTGCTTTTCCCAG-CAA +CCTTCCTAATCTGATCAAACACAGAGAAATGTACTGTT----TCACTCGA +CCTGCCCAACCTCATCACGCACAGAGAGTACTACTGCC----TACCCCGG +CCTGCCCAACCTCATCACGCACAAGGAGTACTACTGCT----TATCCCGC +CCTGCCCAACCTCATCACACACAAGGAGTACTACTGCC----TGACCCGG + +GTCTCCAGATGGATGACAACCT------TCCTGATGTAAATGATAAACAA +GTCTCCAAATGGATGACAATCT------TCCTGATGTAAATGATAAACAA +--CCTCAGTCAGATGA-----T------CCCT----CAAAAGGTGGGCAG +ATGCCTGAAC--ATGATGTTCT------TTCTG---TTGATGGCAAGAAG +CTGCCCGAAC--CCGACG------------------GAGACGACAGACAT +ATGCCTGAGC--ACGACGATACAAACAGTTCGTCGGGCGATGACAGACAC +CTGCCTGAAT--ACGACG---------GTTCAGCGGGGGACGACAGGCAG + +AGCCAAGCCATAAATGATCTCCTAGAAGCCATATATCCA-AGTGTGGACA +AGCCAAGCCATAAGTGATCTCCTAGAAGCCATATATCCA-AGAGTGGACA +AGCCATGCCATCAAAGAACTTCTTCAAGCCATCTATCCACAGAAAGAGCA +AG------CGTGAAAGAACTTCTTGAAGCCATCTACCCTTACT-CCAATA +AGTGTGGTCATGAAGGAGTTATCGGAGGT---ATATCCC-AGAGTC---- +AGTGTGGCCATAAAAGACGCACTGGACGCTAAATATTCC-AGAGCGGAGC +AGCGTAGCCATGAAGGATTTACTGGACGCCATATATCCC-AGATCTGACA + +AACGAGAATATATTATTAA-GCTAGAACCCATAGAAACTAATCAAAATGC +AGAGAGAATATATTATTAA-GCTAGAACCCATAGAAACCAACCAAAATGC +AG-AAAAACAAACAATTCA-GCTTGAGGCCATTGAGACCAACCCCAATGC +AAGAGGAATGTGT-ATTAACACTGGAGCCCATTGCCGGCAACCAGAATGC +--CCGGACTACGTGGTCCG-ACTGGAGCCCATTCGGACCACCAACAAGGC +GGTCGGACTGTGTTGTCCG-GCTCGAGCCCATTCAGAGCACCACCAAGGC +AAGCAGATTACGTCGTCCG-ACTGGAGCCGATTCAAACCAGCACTAAGGC + +AGTATTTCAATATAT-TTCG---AGGACTGAT---AATCCTATTGAAGTC +AGTGTTTCAATATAT-TTCA---AGGACTGAT---AACCCTGCTGAAGTG +AGTGTTCCAACATGT-TTCACT-AGGGGAAATTCAAGACATGCCAGAATC +TGTGTATCAATACCTGTCCA---AAGACCA--------CAGCCTGGCATC +CGTGTTCCAGTACCTCGCCACGGAGGAGGAGCT--GGCCAGGATCCCGTC +CGTGTATCAGTACCTCACCACAGAGGAGGAGCT--GGCCAGATATCCATC +TGTGTTCCAGTACATCAGCACAGAGGAGGAGCT--GGCCAGATATCCATC + +ACA-GAGTCAAGCAGTACT---CCTGAACAAA---CCGAAGTTCAGATA- +ACC-GAGTCAAGCAGTACA---CCTGAACAAA---CTGAAGTTCAAATA- +CCCTGCCCCTACTACTACTGCCCCTGCCCCTGTCCCTGAGATTTTATTA- +T------TCAAGC---------CCTAATCATA--------GCACAAACA- +GCAGACGCCAAGG--------TCGGTGGCGTGCCAATTTGGTTTTGTCG- +ACACACAACCAG----------CGCCAGAGAG-------AGTCCAGTAG- +ACACACACCCAGAGAAAGT--CCGGTGACATGTGAAGGAGAAACCGTTGA + +--C---AGGAAACTAG----CACTGA---------ACAGTCAAAAACAGT +--C---AGGAGACAAG----CTCAGA---------ACAGCTGAAAGCAGT +--CCTGAGAAGAAAAATCGTCGCAAATCTATTTTGGCACCCAAAAA-GGT +--GCTGGGGACACAAC--ATCTCAGA----------CAACCAAGAGCTGT +--TTCAGAGGGAC--------GCGAA-----------AACACGAAGCTCT +--TGTGGGAGGGT--------GAGGC-----------AACAGAAGGCGCC +GGCGCCGGAAGACAAT---CAGCCAA-----------ATCAGCAGGCCGC + +AC--CGGTTACA----GATACAGAGGTGGAAA------CTGTAGAGCCCC +CC--CCGACGCA----GATACAGAGGTGGAGGA---GGCCATAGAGCCTC +CCAACAGTCAGATTTTGAAGATGAGATGGAAACTGAAGTCGAAGAACAAC +AT-------ACA-------------ATGGAGA-----------------T +A--------GCA----------GTGTTGAG-----------CGTGACATT +G--------ACA----------GCAAT--------------CCCACCAAC +A--------GCA----------GAGAGCAGAGA----GAGCCACGGCAGC + +CTCCTGTTG-------AGATT----GTTACAGAT--GA---AGTTGCACC +CTTCTATAG-------AGACT----GTTGTAGAT--GA---AGCTGCAGC +CTGCTAATG-------AAGGTCCGAGCTGC-GAT--GAG-CAAATGAAGA +CCCCTTGGG-------AGAG-----------GAA--GA---AAACGGTTA +TTTCCCCCGGGGCAGAAGAG-----GTGGGAGGC-CGA---GGAGGAGGC +CCGCAAGGGGGACAAGAGAGT----GTCGGTAGTGCGAC--GGAGGAGGA +CC-CGGACAGTATCGAGGAG-----GGCGGAGATGGGAGGCGGAGGAGGA + +TACA------TCTGATGAACAACCTCA----GGAGTCGCAGGCTGACTTG +TCCC------ACTGAGGAGCAACCTCA----GGAATCACAGGCTGACTTG +TTGA------A--GGGGAGGAAGAGGA----AGAGGAGAGTGCAGCCTCA +TATA------CACGATGA--------A----AGAG-AGAACGTTGACATA +GGCAGCGGCGAAGGAGGAGCCGCCGAAGCCCGAGGACGAGGGCTCCACTA +GGCC------AAAGAGGAGCAGCAGCAACCAGAGGACGAAGGCTCCAACA +GTCC------AAAGCGGAGCCGACGCAGCACGAAGACGAGGGCTCCACCA + +GAAACTTC------------------------------------------ +GAGACGTC------------------------------------------ +GAAG---------------------------------------------- +ATAG---------------------------------------------- +GCGGGGT------------------------------------------- +GTGGAGT------------------------------------------- +GCGGGGTAGGCCACCCGAGACTCCGCCAGCACGTTGGACCAAACGCCCTG + +-------------------------TGACAATTCTGATTTTGGTCACCAG +-------------------------TGACAGTTCTGACCTTGGTCACCAG +-------------------------TAAAAGAATTGAG---GATCTCT-- +---------------------------AGAGAGTAGA------------- +--------------------------TGAGGACGTGAC---CATATCC-- +--------------------------GGAAGATGTGAC---CATCTCC-- +CTCACGTCACTTCTTTCGATCGAGGTGGAGGACGTGAC---GATCTCC-- + +TTGATATGTTGTCTTTGTAGAAAAGAATTCAATTCTAGACGAGGTGTTCG +TTGATATGTTGTCTTTGTAGAAAAGAATTCAATTCTAGACGAGGTGTTCG +------TGTTGCCTGTGCGGAAAAGACTTTGGCTCTAGACGTAGTGTGCG +---------------TGCAGACGAAA------------GCAAGGTG---- +------TGCTGTCTGTGCGGTCAGGAATTCAACTCGCGCCGCAGCATCAG +------TGTTGTCTCTGCGGTCAAGACTTCAACTCGCGCCGCAGCATCAG +------TGCTGCCTGTGCGGTCAGGACTTCAACTCGAGGCGCAGCATCCG + +CCGTCACATTCGAAAAGTACACAAGAAAAAGATGGAAGAACTAAAAAAGT +TCGTCACATTCGAAAAGTACACAAAAAAAAGATGGAAGAACTAAAAAAAT +CCGACACTGCCGAAAGATGCATTGGCAGAGGATGGAGGAGCTGCGCAAGT +-CATCAGGATAGTGAAGAACCCGAGGAGACAACAGAAGAA----GCAGGT +ACGCCACTGTCGTAAAGTGCACCAGAACAAGCTGGAAGAGCTGCGGAAGT +GCGCCACTGCCGCAAAATGCACCAGACAAAGCTGGAGGAGCTCAGGAAGT +ACGCCACTGCCGCAAAATGCACCAGACCAAACTGGAGGAGCTCCGCAAGT + +ACATTGAAACACGAA-AGAATCCAAACCAATCCTCTA---------AAGG +ACATTGAAACACGGA-AGACTCCAAACCAGTCTTCAA---------AAGG +TTACAGAGACACGCACAGTGCCC--ATCAGTCTCCTGTCAGTGGTTAAGG +GATCTGGCTTACAAA-TGCATCC-------TCTGCAAC---------AGG +TCACGGAGACGCGTACGGTTCCG--ACCAGCCTGCTGTCTATGG---GAG +TCACCGAGACGCGGACGGTTCCT--ACCAGTCTGCTTTCCATGGTGAAAG +TCACAGAGACGCGCACGGTTCCC--ACGAGCCTGCTGTCCATGGTGAAAG + +AC--GCA----GTAAGAATGTTCTAGTTCCATTAAGTAGGAGTTGTCCAG +AC--GCA----GTAAGAGTGTTCTAGTTTCATTAAGTAGGAGCTGTCCAG +ACAAGCATCCTGTTGAACCACCGCCGTCTCCT--GGGAAGAGCTGCCCAG +ACTTACA--------GAGT-TCGAGGCCACCTTAAAAGACACATGCAGAC +GTCGCCCG-----AGGACACTCAGCACGCCCGCAGGAAAATCCTGCCCGG +GTCGACAG-----AGAACCCTCAGCACACCGACCGGAAAGTCCTGCCCCG +GTCGGCCG-----CGGACGCTCAGCACGCCGACCGGAAAATCCTGCCCAG + +TATGTTGTAAATCATTTGCTACAAAAGCGAATGTAAGGAGGCATTTTGAT +TTTGTTGTAAATCATTTGCTACAAAAGCGAATGTAAGGAGGCATTTTGAT +TGTGCAAAAAGTCATTTGCCACCAAGGCCAATGTTCGTCGTCACTTTGAT +TGTTCATAAGGTTGTGTCCT-------CTAGTTTGACAAGCAAATCTAAG +TGTGTTTCAAAAGCTTCGCCACTAAAGCCAACGTGCGTCGCCATTTTGAC +TGTGCCTCAAGAGCTTTGCAACCAAAGCCAACACCCGGCGCCACTTTGAC +TGTGCCTCAAATCCTTCGCCACCAAAGCCAACGTGCGCCGCCACTTTGAC + +GAAGTTCATAGAGGACTAAGGAGGGATTCAATTACTCCTGATATAGCAAC +GAAGTTCACAGAGGACTAAGGAGGGATTCAATTACTCCTGATATAGCGAC +GAGGTCCACCGTGGCTTAAAGCGGGATTTGATTACTCCAGACATTGCCAC +AAGAT--------GACCAATGGCAAACTTG-------CAGACA--ATCCC +GAGGTGCACCGCGGCCTACGGAGGGACGCCATCACACCCAGCATCGCTTC +GAGGTGCATCGAGGTCTGCGGCGGGATTCTATCACGCCCGCCGTCGCCCT +GAGGTGCATCGCGGCCTGCGGAGGGACACCATCACGCCCAGCATCGCCTC + +AAAGCCTGGGCAACCTTTGTTCCTGGATTCTATTTCTCCT--------AA +AAAGCCTGGGCAGCCTTTGTTCCTGGATTCTGCTTCTCCT--------AA +AAGACCAGGCCAGCCTCTTTTACTTGACACTCCTTCTCCTCCATCTCCAG +AATGCAAGCCCAAGCTCTTCATCTGACTCCCAGAGCTC------------ +GCGCCCCGGCCAGCCTTTCTCTCTGGAGGTCACGCCCCCCCG-----GAA +GAAGCCCGGTCAGCCCTTCCCCCTGGAAACCACGCCTCCGAG-----GAA +GCAGCCTGGCCCGCCCTTTTCTCCGGAGGCCACACCCCCCAG-----CCA + +AAAATCTTTTAAGA----CTCGAAAACAAAAGTCTTCTTCAAAGGCTGAA +AAAATCTTTTAAGA----CTCGCAAACAAAAGTCT---TCAAAGGCTGAA +CAAAAGTACCAAGCTCTCCTTTGAAGCAAGA---------AAAACCACAG +GAAGAATCCCAAGG--------AGAACAAGGATCC------AAAATTCAC +GAGCAACGCCTCCT----CTCCAACGCGCAGCGGCAGCTCCAAGTCCACG +GAGCAATAACTCGT----CGCCGACGCGGAGC--CA----CAAGTCCACT +AAACCAGGCCAAAG----GTCCGA-GCCAGGTG-----TTTGCGGCTTCG + +T--ACAA--TTTAACT-----GCATGCAAATGCCTCCTTTGCAAGAGGAA +T--ACAA--TTTAACT-----GCATGCAAATGCCTCCTTTGCAAGAGGAA +T--ACAA--CCTGACA-----AGTTGCCGCTGCAAGCTCTGCAAACGCAA +T--ATAGGTTTTGACTTCAAGACGTGCTTCTGCAAGCTCTGCAGACGGAC +CCGGCGGCCCCGCCCT------CCAGCCGCTGCGCGCTCTGCAAGAGGAC +CCCGCCGGGACGACCT------CCTGTCGCTGCACGGTTTGCAAGAGGAA +CAGGCGAGCCCTGCCT------CATGCCGCTGCACGCTCTGCAAGAGGAA + +ATATAGTTCACAAATA------ATGCTTAAAAGACATATGCAAATTGTCC +ATACAGTTCACAAATA------ATGCTTAAGAGACATATGCAAATTGTCC +GTACAGCTCCCAACTA------ATGCTTAGGCGACATATGCGAATTGTTC +ATTCAGCTCCGAGCAG------AACCTGGAGAAGCACAT-TGAGCTGCAC +CTACAGCTCTCAGCT------CATGTTGAAGAGGCACATGCGCATCGTCC +CTACAGCTCTCAGCT------CATGTTGAAAAGACACATCCGTATAGTTC +CTACAGCTCCCAGCTAATCTCCATGTTGAAGAGACACATGCGGATTGTTC + +ACAAGATAACTCTTTCTGGAACA-AACTCT-------------------- +ACAAGATAACTCTTTCTGGAGCA-AACTCT-------------------- +ATAAGATA-CCCACTCTAGAAAACAGCTCTCAGAAGTCCAAATCGAAGCA +ACA-GATAAC-------GGTACTGACTTCT-------------------- +ACAAAATA-TACAGTGGCAAAAGTAACAA-------------------CA +ACAAAACC-TACAACATGAAGAGTGACCGG--------------ATCGCA +ACAAAGTA-TACAGCCTGAAGAGCAACAG--------------------- + +--AAAAGAGAAA-AAGGCCC---TAATAATA------CTGCCAACAG-TT +--AAAAGAGAGA-AAGGCCC---TAATAATA------CTGCCAACAG-TT +AGAAAGAAGAGATAAGGTTTATGTAAAGAAAGAGTCTCTCTCGAAAGCTT +-------------------------------------TCGTCAA------ +GCGGCGCCAACGAGGGC-CCGGGCAAC------AACGTCCGGGTGAA--- +GCGAGGCAGACCGCCACACCTGCTAACCCCACCAGTACCAGTGTGAGCCC +------------------CC------------------------------ + +CAGAA-----------ATAAAAGTTAAAGT---TGAACCAGCAGATTCTG +CAGAA-----------GTAAAAGTT---------GAGCTAGCAGATTCTG +CAGAGGATG-------ATGGAAATCAAAGTG--TGAGTT--TTGACTTTA +--------------------------------------------GTTTTA +-AGAGGAGGCG-----GTGAAGGAGGAGGCGGGGAAACCTTCGGACGAAG +CAGCGAAAACGCTGAGGTGAAGGAGGAGCAGGTGGAGCGCTCCGATGAAG +-----------------CAAAGGCGG------------------------ + +T--AGAA-------TCTTCACCCCCTTCCATTA---CCCATTCTCCACAG +T--AGAG-------TCTTCACCCCCTTCCATTA---CCCATTCTCCACAG +AG-AGGA-------TCTACTGCTGGTTGTGTAAACGCCAGTTTAGTACCA +---------------CTGCTGTCCGCTCTGCCA----CTAT--------- +ACGAGGA------CTTCGACAGCAGTCCCGCC-----CCGTCCCCCGTCC +AGGAGGAGGAGGACTCTGACAGCAGTCCCGCC-----CCGTCTCCCGGTG +----------------CGCCATCCCTCCCGCCG----TCGTCCTCCCGCG + +AATG---------AATTAAAGGG---------AACAAATCA------TTC +AATG---------AACTCAAGGG---------AACAAATCA------TTC +GTTAC--------AACCTAGGCA---------AACACATTGCAGAGCTCC +---------------------AA---------AACACGCCG--------C +AGAGCGCCGGGCCGACCAAAG-GCGTTT--CCGTGGCACCCAACGCCGTG +ACAGCGCCGGCACAGCTAAAGCGGGTTTGACTAACGCACCGAAAGAAGAA +GCAGC---------------------------AACGCGCC---------- + +AAA-TGAAAAAAAGAACACA-CCGGCAG-CACAGAAAAA-TAAAGTT--- +AAA-TGAAAAAAAGAACACA-CCAGCAA-CACAGAAAAA-CAAAGTT--- +ACACTGATGGAAACGATAG---CATCTA-CATAAAGTTT-TACCGCTGCC +AA---GAGAGATGTGCTGCG-CCATCT--CTCAGACTTC-CA-------- +AAGGTGAAGGAGGCGGAGGCCCCGTCGAGCCCAAAGG---CCGCGCCG-- +GAGGAGGAGGAAGAGGAGCAGCCAGCAAGCCCAAAGGTGGCAGCGCCG-- +-------------------------------------------CGCC--- + +--------AAACAAGACTCTGAAAGCCCTAAA--TCAACTAGTCCGTCG- +--------AAACAGGACTCTGAAAGCCCTAAA--TCAGCTAGCCCTTCG- +CCATCTGCAGATATGAGTC---ACGGCGTAAACGTGATGTAATTCGCCAT +-----------CAAGA-------------AGA--------AATCC----- +-----------TCGTTGTCGGC---------------CGCCGCCAT---- +-----------CCGCCGTCCGCTTCCCGTGCGGACAACGGCGCCACTGG- +-----------TCG------------------------GGAGCTTC---- + +GCTGCAGGTGGCCAGCAAAAAACC----AGAAAACCA---AAACTTTCAG +GCTGCAGGTGGCCAGCAAAAAACC----AGGAAACCA---AAACTTTCAG +ATCACAG-TGGTGCACAAGAAGTCGTCGAGGTATCTGGCTAAAGTCATGC +-TTGTACTTG---AGCAAGA--TC--------------------TCCCAG +------CCT---CCCCAAAACCAC---------------CAAACTGTCGG +---CAACCTGGCTGCCAAAATATC---------------CAAACTGTCGG +-------CT-----CAAAAATGAG---------------CAAACTGTCGG + +CTGGCTTTGACT-TTAAGCAACTTTACTGTAAACTTTGTAAACGTCAGTT +CTGGCTTTGACT-TTAAGCAACTTTACTGTAAACTCTGTAAACGCCAGTT +CTGCCTTGGAGAACCAGGCAG--TTA--AGAAAC-CGGCTGATGCTATCT +TCG--CTGGAGGACTATTCAA--TCA--AGAAGC-CAGCGGATGTTGTGT +TGGGCTTTGACT-TCAAGCAGCTCTTCTGCAAGCTGTGCAAGCGGCAGTT +TGGGTTTTGACT-TGGAGCAGCTCTTCTGCAAGCTCTGCAAACGGCAGTT +TGGGTTTCGACT-TCAAGCAGCTCTACTGCAAACTTTGCAAGCGTCAGTT + +TA--CTTC-CAAACAGAACTTGACTAAACACATCGAGTTGCACACAGATG +TA--CTTC-CAAGCAGAACTTGACTAAACACATTGAGTTGCACACAGATG +TGAGCAGCGCAAGCAAGA---AAATAAATGCA--AAGGAGGATGGCAGTG +TG---------AGCAAGG-----ATCTGTCCA--AAGATCGAGATCAACA +CAGCTCGC---GGCAGAACCTCACGAAACACATCGAGCTGCACACGGACG +CAGCTCCC---GTCAGAATCTGACCAAGCACATCGAGCTCCACACCGACG +CAGCTCGC---GGCAGAATCTGACCAAACACATCGAGCTGCACACGGACG + +GAAATAACATTTATGTTAAATTCTACAAGTGTCCTCT--TTG-CACTTAT +GAAATAACATTTATGTTAAGTTCTACAAGTGTCCTCT--CTG-CACTTAC +GGAA--GCATAAAACACAAGATCCACCAGCCTCCCCTAGCAGTCGCCAAC +GGAGT----TAAAAGCTAA---CTCCAAGCATGCTT-------CGCCA-- +GCAACGACATCTTCATCAAGTTCTACCGCTGCCCCCT--CTGCCGCTA-C +GCAACGACATCTTCATCAAGTTCTACCGCTGTCCTCT--CTGCCGCTA-C +GCAACGACATCTTCATCAAGTTCTACCGCTGCCCTCT--CTGTCGCTA-C + +GAAACTCGTCGGAAACGTGATGTGATACGACATATAACTGTGGTTCATAA +GAAACCCGTCGGAAACGTGATGTGATAAGACATATAACTGTGGTTCATAA +AAGATCTTTTAG------TATCTCCCAAAGCAAAGAAACAGGAATCACAA +------------------TACGTGACACG--AAAGAACC-TGA--CGAAA +GAGTCGCGGCGCAAGCGTGACGTCCTGCGCCACGTCACGGTGGTCCACAA +GAGTCCCGCCGCAAGCGCGACGTCCTGCGCCACGTGACCGTCGTTCACAA +GAGTCGCGCCGCAAACGCGACGTCCTGCGCCACGTCACGGTCGTCCACAA + +AAAGTCATCTCGTTATCTTGGGAAAATAACAGCCAGTTTAGAGATCAGAG +AAAGTCATCTCGTTACCTTGGGAAAATCACAGCCAGTTTAGAGATCAGAG +A----CATCCCCTAACACTCGAAAG----CATTCCGCTTTAACATCA--- +ACAG-CACTGCGCAAC------AAG---------ACCTTAAAGACTGG-- +GAAGACCTCGGCGTACCTCGGGAAGATCATGCCCAAGCTGGAAAGCCGGG +GAAGTCCTCCACGTACCTGGCCAAGATCATGCCCAAACTGGAGAGCCGGG +GAAGTCCTCGGCTTACCTCGCCAAGATCATGCCCAAGCTGGAGAGCAGGG + +CTATAAAAAAGCCTA--TTGATTTT--GTTCTAAATAAAGT--------- +CTATAAAAAAGCCTA--TTGATTTT--GTTCTAAACAAAGT--------- +CT-TAACACCGGCAAACTTGAGTCTCCGCTTGCACCAAACA--------- +---TAATAAGGTGCA--------------CCACAAAAAGGA--------- +CGGTGAAGAGGCTCG--CCGAGGCC--GTCCTCAACAGCAC--------- +CGGTGAAGCGGCTGG--CCGAGGTG--GTCCTCAGCAGC----------- +CGGTGAAGAGGCTGG--CGGAGGTG--GTCCTCAGCAGCACCAGCGCCAC + +-GGC-------AAAAAGAGGCCCTT------------------------- +-GGC-------AAAAAGAGGCCCTT------------------------- +-GAC-------AAGACAAGAACCTT------------------------- +-AGT-------GAAAAAAG------------------------------- +-GTC---CCCGAACAAGAGGCC---------------------------- +--TC---C---AACAAGAGGAC---------------------------- +CGTCACTCGCAAGCAGGAGGGCTCCGCGGCGACCCCGTCCGCCTCCGCAG + +----------------------------------------CGAGGGATGA +----------------------------------------CAAGGGAGGA +----------------------------------------CAAGCTGCCA +-------------------------------------------------- +-----------------------------------------GAGCGGCGG +-----------------------------------------GAGCAGCAA +CCTGCTCCTCGTCCTCGCAGGTCCCCTCAACCGCCACTCGCAAGCAGCAG + +----------------------------------------------AGCA +----------------------------------------------AGCA +----------------------------------------------AG-A +-------------------------------------------------- +----CGTCA-------------------------------------AGGA +----CGGCA-------------------------------------ACCA +GACCCGTCATCGCCCACGGTCCCGGCGTCCACGCCCGTCACCCGTAAGCA + +AAACATA-GTGATTCAAAA---CATGATGGCACTTCTAACTCTCCTAGTA +AAACATA-ATGACTCAAAA---CAGGATGGCACTTCCAATTCTCCAAGTA +ATCCACATGTCACTCGAAGT--CATAATGTTATCAAGGGACCACCCATCA +--------------CGAAG---CCTGATAGC------------CCCA--- +GGAG-GTGAACGGGCGC-----CACGTGTCCTC--GTCCTCCTCGTCCTC +GGCC-CCCAACACCCGCAG--GCACGAGTCCGG--ATC------------ +GGAGAGACAGCAGACGCAGCTGCACCGGCCCCTCAGCCCGCCGCTCACTC + +AAAAGTATGA--------------------------------AGT-AGCT +AAAAGTATGA--------------------------------AGT-AGCC +CCA-----GA--------------------------------AGTCAGGA +-------------------------------------------------- +CTCCCCCTCG-------------------------------CCGCCCGTC +-------TGA-------------------------------CAGCAGGGC +GCCGCAGTGAAAAGCACCAGCGCAGTTGCTCCCGCGCCGCCTCGCCCGGC + +GACGTCG------------------------------------------- +GACGTCG------------------------------------------- +GACTT--------------------------------------------- +-------------------------------------------------- +ACCCCC-------------------------------------------- +GTC--C-------------------------------------------- +GCCCACACGCCACACACGCGGCGCCATGACGCCCAGTCAGACGGTGGCGG + +--------GTATTGAAGTAAAAGTCACAAAAAACTTTTCTCTTCACAGAT +--------GTATTGAAGTGAAAGTCACAAAAAACTTTTCTCTTCACAGAT +--------GTACTGAGGTTAGAGTAACCAAAAACTTTTCCCTCCATGCGT +--------------AAGGCAGTGTCACCAAGAAAT---CAGTGCATGTGT +-------TCCACCGAAGTCAGAGTGACCAAGAACTTCTCCCTCCATGCCT +-------TCCACCGAAGTCAAAGTGACGAAAAACTTCTCCCTGCATGCGT +GACGTCGTCCACTGAGGTCAGGGTGACCAAGAACTTCTCGCTGCACGCCT + +GCAATAAATGTGGAAAGGCATTTGCCAAAAAGACTTACCTTGA-ACATCA +GCAATAAATGTGGAAAGGCATTTGCCAAAAAGACTTACCTTGA-ACATCA +GCGATATGTGTGGCAGAGCATTTGCCAAAAAGGTTTACCTTGAGACA-CA +GTGACGTCTGTGGGGAGAGCTTCATGAAGACAAGGTATCTGGG-GTTGCA +GCGACCAGTGTGGACGGGCCTTTGCCAAGAAGCTGTACCTGGA-GTCTCA +GCGATCAGTGTGGGCGGGCCTTCGCCAAGAAGCTTTATTTGGA-ATCTCA +GCGACCAGTGCGGACGCGCCTTCGCCAAAAAGCTGTATCTGGA-GTCTCA + +TAAGAAAACTCATAAGGCAAATGCTTCCAATTCACCTGAAGGAAACAAAA +TAAGAAAACTCATAAGGCAAATGCTACCAATTCACCTGAAGGAAACAAAA +CAGGCGGAGACACAAGAC---TGCCATTG------CTAGTGGGGACAAAT +CAAGAGAATGCATCTGAAAACCGCATCCA------------GGAGCG--- +CAAGCGCAGTCATCGCAACGCGGCGACGG------CGGCGGCCAGCAGGA +CAAGCGAAGTCATCGGAACGCGGCGGTGG------CGGCAGCCAGCAGGA +CAAGCGCAGCCATCGCAACGCACCAACCG------CAGCGGCTAACAGGC + +CCAAAGGCCGAAGTACAAGATCTAAGGCTCTTGTCTGA +CCAAAGGCCGAAGTACAAGATCTAAGGCTCTTGTCTGA +TACAAGGAAGAAGCACTCGATCAAAGGCTCTCATTTGA +CAGGAGTCAGAA---CTAGGTCAAAGGCCATGCTTTGA +GGAAAGGAGTCAGCACCCGCTCCAAGTCCCTGGTC--- +GGAAAGGTGTCAGCACGCGCTCCAAGTCCCTGATG--- +GCAAGGGAGTCAGCACCCGCTCCAAGACCCTGGCC---; +end; + diff --git a/debian/phyml.examples b/debian/phyml.examples index e39721e..dd1d6f3 100644 --- a/debian/phyml.examples +++ b/debian/phyml.examples @@ -1 +1,2 @@ examples/* +debian/phyml-examples/* diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test index 32b94b5..656be61 100644 --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -20,6 +20,6 @@ echo "AA interleaved sequence file, default parameters :" /usr/bin/phyml -i proteic -d aa echo "AA sequential sequence file, with customization :" -/usr/bin/phyml -i nexus_example.nxs -q -d aa -m JTT -c 4 -a e +/usr/bin/phyml -i example.nex -d nt -c 4 -a e echo "PASS" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit