[Biojava-dev] [Bug 2679] NEXUS parse fails on extraneous comma (TREES/TRANSLATE)
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Nov 21 10:50:10 UTC 2008
http://bugzilla.open-bio.org/show_bug.cgi?id=2679
------- Comment #2 from keesey at gmail.com 2008-11-21 05:50 EST -------
#NEXUS
[File created by TreeBASE: 1/29/99 19:24:10]
[Matrix accession#: M474]
BEGIN DATA;
DIMENSIONS NTAX=34 NCHAR=223;
[!This data set was downloaded from TreeBASE, a prototype relational database
of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard
University, and UC Davis. Please do not remove this acknowledgment from the
Nexus file.
TreeBASE © 1994-1999.
Study reference:
Bininda-Emonds, O. R. P., J. L. Gittleman, and A. Purvis. 1999. Building larger
phylogenies using supertrees: a complete phylogeny of the extant Carnivora
(Mammalia). Biological Reviews, in press.
Study accession number = S355
Matrix accession number = M474
]
FORMAT MISSING = ? GAP = - INTERLEAVE ;
MATRIX
'Vulpes_zerda'
1?000111000????0000?1100000000?1001???????001100000?????10000000000000111000??????1000000????????111
'Vulpes_vulpes'
1?110000000?00??????1100000000?1001???????110000000?1???10000000000000110101??????1100000???0000?110
'Vulpes_velox'
1?111000000????0000?1100000000?1001???????110000000?????10000000000000110110??????1100000????????110
'Vulpes_rueppelli'
1???????????????????1100000000?1001???????110000000?????10000000000000110101??????1100000????????110
'Vulpes_pallida'
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_ferrilata'
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Vulpes_corsac'
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000????????110
'Vulpes_chama'
1???????????????????1100000000?1001???????110000000?????10000000000000110000??????1100000????????100
'Vulpes_cana'
1???????????????????1100000000?1001???????110000000?????10000000000000111000??????1100000????????111
'Vulpes_bengalensis'
1???????????????????1100000000?1001???????110000000???????????????????????????????1100000???????????
'Urocyon_littoralis'
1??????????????????????????????1001???????001110000???????????????????????????????1010000???????????
'Urocyon_cinereoargenteus'
1?000110000?????????1010000000?1001?0?000?001110000?????00000000000000000000??????1010000?0?1000?000
'Speothos_venaticus'
1?000100111?????????0001100110?0000?????????????????????11100011100000000000?1100?0001000???????????
'Pseudalopex_vetulus'
1???????????????????0001111000?1000???????001001010??????????????????????????0000?0001000???????????
'Pseudalopex_sechurae'
1???????????????????0001111000?1010???????001001010??????????????????????????0010?0001101???????????
'Pseudalopex_gymnocercus'
1???????????????????0001111000?1010???????001001010?????11111000000000000000?0010?0001101???????????
'Pseudalopex_griseus'
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0010?0001101???????????
'Pseudalopex_culpaeus'
1???????????????????0001111000?1010???????001001010?????11111100000000000000?0011?0001101???????????
'Otocyon_megalotis'
1?000111000?????????1010000000?0000???????100000000?????11000000000000000000??????1000000???????????
'Nyctereutes_procyonoides'
1?100000000?????????0001100101?0000???????100000000?1???10000000000000100000????????????????????????
'Lycaon_pictus'
1??????????????1000????????????0000???000???????????????11100011100000000000??????0001000???1110????
'Dusicyon_australis'
1???????????????????0001110000?1000???????001001010??????????????????????????0011?0001100???????????
'Cuon_alpinus'
1??????????????????????????????0000?????????????????????11100010010000000000??????0001000???????????
'Chrysocyon_brachyurus'
1?000100110?????????0001000000?0000???????001001100?????11100011000000000000?0000?0001000???????????
'Cerdocyon_thous'
1?000100111?????????0001100101?1000?????????????????????11110000000000000000?1000?0001000???????????
'Canis_simensis'
1??????????????????????????????1100???111?001000001???0?11100010011011000000??????0001110???????????
'Canis_rufus'
1??????????????????????????????1100???????001000001???0???????????????????????????0001110???????????
'Canis_mesomelas'
1???????????10?1100????????????1100???100?001000001???0?11100010010000000000??????0001110???????????
'Canis_lupus'
1?000100100?11?1111????????????1100?1?111?001000001?0?1?11100010011010000000??????0001110?1?1111????
'Canis_latrans'
1???????????11?1111????????????1100?1?111?001000001???1?11100010011011000000??????0001110?1?1111????
'Canis_aureus'
1??????????????1110????????????1100???110?001000001???0?11100010011100000000??????0001110???1100????
'Canis_adustus'
1??????????????1000????????????1100???000?001000001???0?11100010011100000000??????0001110???????????
'Atelocynus_microtis'
1???????????????????0001100110?1000???????001001100??????????????????????????1100?0001000???????????
'Alopex_lagopus'
1?111000000????????????????????1000???????110000000?????10000000000000110110??????1000000????????110
'Vulpes_zerda'
0000?11111000?11110000?00000010??????????10000?01???????????????????100000?????0001?1000001010000000
'Vulpes_vulpes'
1011?11110100?11101101?00000010????????????????01?0000110???00001???100010?????0001?1000001000000000
'Vulpes_velox'
1100?11110111?11101110?00000011????????????????01???????????00001???100010?????0001?1000001000000000
'Vulpes_rueppelli'
1011?11110110?11101101?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_pallida'
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_ferrilata'
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_corsac'
1010?11110100?11101100?????????????????????????01???????????00001???100010?????0001?1000001100000000
'Vulpes_chama'
0000?11100000?11101000?00000010????????????????01???????????00001???100010?????0001?1000001011000000
'Vulpes_cana'
0000?11111000?11110000?????????????????????????01???????????00001???100010?????0001?1000001010100000
'Vulpes_bengalensis'
???????????????????????????????????????????????01???????????00001???100010?????0001?1000001011000000
'Urocyon_littoralis'
?????????????????????????????????????????11000?01???????????????????100100?????0010?1000001000010000
'Urocyon_cinereoargenteus'
0000?10000000?10000000?00000000??????????11000?01???????????????????100100?????0010?1000001000010000
'Speothos_venaticus'
???????????????????????11001000??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Pseudalopex_vetulus'
???????????????????????11110000??????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_sechurae'
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001101
'Pseudalopex_gymnocercus'
?????????????????????????????????????????00101?01?1100000???????????101000?????0100?1000000000001110
'Pseudalopex_griseus'
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001100
'Pseudalopex_culpaeus'
?????????????????????????????????????????00101?01???????????????????101000?????0100?1000000000001110
'Otocyon_megalotis'
?????11000000?11000000?00000000????????????????00?0000001???????????100000?????0000?0000000000000000
'Nyctereutes_procyonoides'
???????????????????????00000000????????????????01?0000001???????????100000?????0000?0000000000000000
'Lycaon_pictus'
???????????????????????11001100??????????00100?10?0000000???????????000001?????0000?0000000000000000
'Dusicyon_australis'
?????????????????????????????????????????00101?01???????????????????100000?????0000?1000000000001000
'Cuon_alpinus'
???????????????????????????????????????????????10???????????????????000001?????0000?0000000000000000
'Chrysocyon_brachyurus'
???????????????????????11100000??????????00100?01?0000100???????????100000?????0000?0000000000000000
'Cerdocyon_thous'
???????????????????????11110000????????????????01???????????????????100000?????0000?1000000000001000
'Canis_simensis'
?????????????????????????????????????????00110?01???????????????????110000?????1000?1110000000000000
'Canis_rufus'
??????????????????????????????????100?10?00110?01?????????1?11100?1?110000???1?1000?1100110000000000
'Canis_mesomelas'
???????????????????????11001000?1?011?11?00110?01?1110000???11010???110000?0???1000?1111000000000000
'Canis_lupus'
?????00000000?00000000?11001100?1?100????00110?01?1001000?1?11100?1?110000???1?1000?1100110000000000
'Canis_latrans'
???????????????????????11001100???010?00?00110?01?1001000???10000?1?110000???1?1000?1100100000000000
'Canis_aureus'
??????????????????????????????????011?11?00110?01???????????11010?0?110000?1?0?1000?1110000000000000
'Canis_adustus'
?????????????????????????????????????????00110?01?1110000???11010???110000?1???1000?1111000000000000
'Atelocynus_microtis'
?????????????????????????????????????????00100?01???????????????????100000?????0000?1000000000001000
'Alopex_lagopus'
1100?11111111?11101110?00000011?0??????????????01?0000110???00001???100000?????0000?1000001000000000
'Vulpes_zerda' ?????????11000000000000
'Vulpes_vulpes' ?????????11000000000000
'Vulpes_velox' ?????????11000000000000
'Vulpes_rueppelli' ???????????????????????
'Vulpes_pallida' ?????????11000000000000
'Vulpes_ferrilata' ????????????????????0??
'Vulpes_corsac' ?????????11000000000000
'Vulpes_chama' ?????????11000000000000
'Vulpes_cana' ???????????????????0???
'Vulpes_bengalensis' ?????????11000000000000
'Urocyon_littoralis' ???????????????????????
'Urocyon_cinereoargenteus' ???0?????10100000000000
'Speothos_venaticus' ?????????00010001101101
'Pseudalopex_vetulus' ?????????00010001101000
'Pseudalopex_sechurae' ?????????00010001000000
'Pseudalopex_gymnocercus' ?????????00010001000000
'Pseudalopex_griseus' ?????????00010001000000
'Pseudalopex_culpaeus' ?????????00010001110000
'Otocyon_megalotis' ?1???????10100000000000
'Nyctereutes_procyonoides' ?????????00010001101110
'Lycaon_pictus' ?0???????00011010000000
'Dusicyon_australis' ?????????00010001110000
'Cuon_alpinus' ?????????00011010000000
'Chrysocyon_brachyurus' ?????????00010001101000
'Cerdocyon_thous' ?????????00010001101110
'Canis_simensis' ?????????00011100000000
'Canis_rufus' ?????1?1?00011100000000
'Canis_mesomelas' ?????????00011100000000
'Canis_lupus' ?1?1?1?1?00011100000000
'Canis_latrans' ???1?1?0?00011100000000
'Canis_aureus' ?????????00011100000000
'Canis_adustus' ?????????00011100000000
'Atelocynus_microtis' ?????????00010001101101
'Alopex_lagopus' ?????????11000000000000
;
END;
BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ;
END;
BEGIN TREEBASE;
END;
BEGIN TREES;
[! 1 trees. TreeBASE accession#: Tree1118 ]
TRANSLATE
1 'Nyctereutes_procyonoides',
2 'Urocyon_cinereoargenteus',
3 'Pseudalopex_gymnocercus',
4 'Chrysocyon_brachyurus',
5 'Pseudalopex_sechurae',
6 'Pseudalopex_culpaeus',
7 'Pseudalopex_vetulus',
8 'Atelocynus_microtis',
9 'Pseudalopex_griseus',
10 'Dusicyon_australis',
11 'Urocyon_littoralis',
12 'Vulpes_bengalensis',
13 'Speothos_venaticus',
14 'Otocyon_megalotis',
15 'Vulpes_ferrilata',
16 'Vulpes_rueppelli',
17 'Canis_mesomelas',
18 'Cerdocyon_thous',
19 'Alopex_lagopus',
20 'Vulpes_pallida',
21 'Canis_simensis',
22 'Vulpes_corsac',
23 'Canis_latrans',
24 'Lycaon_pictus',
25 'Canis_adustus',
26 'Vulpes_vulpes',
27 'Vulpes_chama',
28 'Vulpes_velox',
29 'Vulpes_zerda',
30 'Canis_aureus',
31 'Cuon_alpinus',
32 'Pseudalopex',
33 'Canis_rufus',
34 'Vulpes_cana',
35 'Canis_lupus',
36 'Canidae',
37 'Canis',
;
TREE 'Fig._9' = [&R]
(((((((19,28),((22,15),(16,26))),(34,29)),(12,27,20)),(2,11)),14),((8,(((25,30),17),(23,(35,33),21)),18,4,31,(10,((6,9,3,5),7)),24,13),1));
END;
--
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
More information about the biojava-dev
mailing list