| blob | 99998af5916de38bcfcca446c5bf9c3de25c5b39 |
1 #NEXUS
4 BEGIN DATA;
5 DIMENSIONS NTAX=12 NCHAR=898;
7 [!A portion of primate mitochondrial DNA. Site names correspond to Anderson (1981) numbering scheme.
9 This portion includes parts of two protein-coding genes, as well as 3 tRNA's:
11 tRNA His: 459-528
12 tRNA Ser (AGY): 529-588
13 tRNA Leu (CUN): 589-659
15 Data from:
17 Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol., 5:626-644.
19 See pp. 335-339 of the MacClade book.]
20 FORMAT DATATYPE=DNA MISSING=? GAP=- MATCHCHAR=. INTERLEAVE ;OPTIONS IGNORE=UNINFORM ;
22 CHARLABELS
23 [1] A_11680 [2] A_11681 [3] A_11682 [4] A_11683 [5] A_11684
24 [6] A_11685 [7] A_11686 [8] A_11687 [9] A_11688 [10] A_11689
25 [11] A_11690 [12] A_11691 [13] A_11692 [14] A_11693 [15] A_11694
26 [16] A_11695 [17] A_11696 [18] A_11697 [19] A_11698 [20] A_11699
27 [21] A_11700 [22] A_11701 [23] A_11702 [24] A_11703 [25] A_11704
28 [26] A_11705 [27] A_11706 [28] A_11707 [29] A_11708 [30] A_11709
29 [31] A_11710 [32] A_11711 [33] A_11712 [34] A_11713 [35] A_11714
30 [36] A_11715 [37] A_11716 [38] A_11717 [39] A_11718 [40] A_11719
31 [41] A_11720 [42] A_11721 [43] A_11722 [44] A_11723 [45] A_11724
32 [46] A_11725 [47] A_11726 [48] A_11727 [49] A_11728 [50] A_11729
33 [51] A_11730 [52] A_11731 [53] A_11732 [54] A_11733 [55] A_11734
34 [56] A_11735 [57] A_11736 [58] A_11737 [59] A_11738 [60] A_11739
35 [61] A_11740 [62] A_11741 [63] A_11742 [64] A_11743 [65] A_11744
36 [66] A_11745 [67] A_11746 [68] A_11747 [69] A_11748 [70] A_11749
37 [71] A_11750 [72] A_11751 [73] A_11752 [74] A_11753 [75] A_11754
38 [76] A_11755 [77] A_11756 [78] A_11757 [79] A_11758 [80] A_11759
39 [81] A_11760 [82] A_11761 [83] A_11762 [84] A_11763 [85] A_11764
40 [86] A_11765 [87] A_11766 [88] A_11767 [89] A_11768 [90] A_11769
41 [91] A_11770 [92] A_11771 [93] A_11772 [94] A_11773 [95] A_11774
42 [96] A_11775 [97] A_11776 [98] A_11777 [99] A_11778 [100] A_11779
43 [101] A_11780 [102] A_11781 [103] A_11782 [104] A_11783 [105] A_11784
44 [106] A_11785 [107] A_11786 [108] A_11787 [109] A_11788 [110] A_11789
45 [111] A_11790 [112] A_11791 [113] A_11792 [114] A_11793 [115] A_11794
46 [116] A_11795 [117] A_11796 [118] A_11797 [119] A_11798 [120] A_11799
47 [121] A_11800 [122] A_11801 [123] A_11802 [124] A_11803 [125] A_11804
48 [126] A_11805 [127] A_11806 [128] A_11807 [129] A_11808 [130] A_11809
49 [131] A_11810 [132] A_11811 [133] A_11812 [134] A_11813 [135] A_11814
50 [136] A_11815 [137] A_11816 [138] A_11817 [139] A_11818 [140] A_11819
51 [141] A_11820 [142] A_11821 [143] A_11822 [144] A_11823 [145] A_11824
52 [146] A_11825 [147] A_11826 [148] A_11827 [149] A_11828 [150] A_11829
53 [151] A_11830 [152] A_11831 [153] A_11832 [154] A_11833 [155] A_11834
54 [156] A_11835 [157] A_11836 [158] A_11837 [159] A_11838 [160] A_11839
55 [161] A_11840 [162] A_11841 [163] A_11842 [164] A_11843 [165] A_11844
56 [166] A_11845 [167] A_11846 [168] A_11847 [169] A_11848 [170] A_11849
57 [171] A_11850 [172] A_11851 [173] A_11852 [174] A_11853 [175] A_11854
58 [176] A_11855 [177] A_11856 [178] A_11857 [179] A_11858 [180] A_11859
59 [181] A_11860 [182] A_11861 [183] A_11862 [184] A_11863 [185] A_11864
60 [186] A_11865 [187] A_11866 [188] A_11867 [189] A_11868 [190] A_11869
61 [191] A_11870 [192] A_11871 [193] A_11872 [194] A_11873 [195] A_11874
62 [196] A_11875 [197] A_11876 [198] A_11877 [199] A_11878 [200] A_11879
63 [201] A_11880 [202] A_11881 [203] A_11882 [204] A_11883 [205] A_11884
64 [206] A_11885 [207] A_11886 [208] A_11887 [209] A_11888 [210] A_11889
65 [211] A_11890 [212] A_11891 [213] A_11892 [214] A_11893 [215] A_11894
66 [216] A_11895 [217] A_11896 [218] A_11897 [219] A_11898 [220] A_11899
67 [221] A_11900 [222] A_11901 [223] A_11902 [224] A_11903 [225] A_11904
68 [226] A_11905 [227] A_11906 [228] A_11907 [229] A_11908 [230] A_11909
69 [231] A_11910 [232] A_11911 [233] A_11912 [234] A_11913 [235] A_11914
70 [236] A_11915 [237] A_11916 [238] A_11917 [239] A_11918 [240] A_11919
71 [241] A_11920 [242] A_11921 [243] A_11922 [244] A_11923 [245] A_11924
72 [246] A_11925 [247] A_11926 [248] A_11927 [249] A_11928 [250] A_11929
73 [251] A_11930 [252] A_11931 [253] A_11932 [254] A_11933 [255] A_11934
74 [256] A_11935 [257] A_11936 [258] A_11937 [259] A_11938 [260] A_11939
75 [261] A_11940 [262] A_11941 [263] A_11942 [264] A_11943 [265] A_11944
76 [266] A_11945 [267] A_11946 [268] A_11947 [269] A_11948 [270] A_11949
77 [271] A_11950 [272] A_11951 [273] A_11952 [274] A_11953 [275] A_11954
78 [276] A_11955 [277] A_11956 [278] A_11957 [279] A_11958 [280] A_11959
79 [281] A_11960 [282] A_11961 [283] A_11962 [284] A_11963 [285] A_11964
80 [286] A_11965 [287] A_11966 [288] A_11967 [289] A_11968 [290] A_11969
81 [291] A_11970 [292] A_11971 [293] A_11972 [294] A_11973 [295] A_11974
82 [296] A_11975 [297] A_11976 [298] A_11977 [299] A_11978 [300] A_11979
83 [301] A_11980 [302] A_11981 [303] A_11982 [304] A_11983 [305] A_11984
84 [306] A_11985 [307] A_11986 [308] A_11987 [309] A_11988 [310] A_11989
85 [311] A_11990 [312] A_11991 [313] A_11992 [314] A_11993 [315] A_11994
86 [316] A_11995 [317] A_11996 [318] A_11997 [319] A_11998 [320] A_11999
87 [321] A_12000 [322] A_12001 [323] A_12002 [324] A_12003 [325] A_12004
88 [326] A_12005 [327] A_12006 [328] A_12007 [329] A_12008 [330] A_12009
89 [331] A_12010 [332] A_12011 [333] A_12012 [334] A_12013 [335] A_12014
90 [336] A_12015 [337] A_12016 [338] A_12017 [339] A_12018 [340] A_12019
91 [341] A_12020 [342] A_12021 [343] A_12022 [344] A_12023 [345] A_12024
92 [346] A_12025 [347] A_12026 [348] A_12027 [349] A_12028 [350] A_12029
93 [351] A_12030 [352] A_12031 [353] A_12032 [354] A_12033 [355] A_12034
94 [356] A_12035 [357] A_12036 [358] A_12037 [359] A_12038 [360] A_12039
95 [361] A_12040 [362] A_12041 [363] A_12042 [364] A_12043 [365] A_12044
96 [366] A_12045 [367] A_12046 [368] A_12047 [369] A_12048 [370] A_12049
97 [371] A_12050 [372] A_12051 [373] A_12052 [374] A_12053 [375] A_12054
98 [376] A_12055 [377] A_12056 [378] A_12057 [379] A_12058 [380] A_12059
99 [381] A_12060 [382] A_12061 [383] A_12062 [384] A_12063 [385] A_12064
100 [386] A_12065 [387] A_12066 [388] A_12067 [389] A_12068 [390] A_12069
101 [391] A_12070 [392] A_12071 [393] A_12072 [394] A_12073 [395] A_12074
102 [396] A_12075 [397] A_12076 [398] A_12077 [399] A_12078 [400] A_12079
103 [401] A_12080 [402] A_12081 [403] A_12082 [404] A_12083 [405] A_12084
104 [406] A_12085 [407] A_12086 [408] A_12087 [409] A_12088 [410] A_12089
105 [411] A_12090 [412] A_12091 [413] A_12092 [414] A_12093 [415] A_12094
106 [416] A_12095 [417] A_12096 [418] A_12097 [419] A_12098 [420] A_12099
107 [421] A_12100 [422] A_12101 [423] A_12102 [424] A_12103 [425] A_12104
108 [426] A_12105 [427] A_12106 [428] A_12107 [429] A_12108 [430] A_12109
109 [431] A_12110 [432] A_12111 [433] A_12112 [434] A_12113 [435] A_12114
110 [436] A_12115 [437] A_12116 [438] A_12117 [439] A_12118 [440] A_12119
111 [441] A_12120 [442] A_12121 [443] A_12122 [444] A_12123 [445] A_12124
112 [446] A_12125 [447] A_12126 [448] A_12127 [449] A_12128 [450] A_12129
113 [451] A_12130 [452] A_12131 [453] A_12132 [454] A_12133 [455] A_12134
114 [456] A_12135 [457] A_12136 [458] A_12137 [459] A_12138 [460] A_12139
115 [461] A_12140 [462] A_12141 [463] A_12142 [464] A_12143 [465] A_12144
116 [466] A_12145 [467] A_12146 [468] A_12147 [469] A_12148 [470] A_12149
117 [471] A_12150 [472] A_12151 [473] A_12152 [474] A_12153 [475] A_12154
118 [476] A_12155 [477] A_12156 [478] A_12157 [479] A_12158 [480] A_12159
119 [481] A_12160 [482] A_12161 [483] A_12162 [484] A_12163 [485] A_12164
120 [486] A_12165 [487] A_12166 [488] A_12167 [489] A_12168 [490] A_12169
121 [491] A_12170 [492] A_12171 [493] A_12172 [494] A_12173 [495] A_12174
122 [496] A_12175 [497] A_12176 [498] A_12177 [499] A_12178 [500] A_12179
123 [501] A_12180 [502] A_12181 [503] A_12182 [504] A_12183 [505] A_12184
124 [506] A_12185 [507] A_12186 [508] A_12187 [509] A_12188 [510] A_12189
125 [511] A_12190 [512] A_12190a [513] A_12191 [514] A_12192 [515] A_12193
126 [516] A_12194 [517] A_12195 [518] A_12196 [519] A_12197 [520] A_12198
127 [521] A_12199 [522] A_12200 [523] A_12201 [524] A_12202 [525] A_12203
128 [526] A_12204 [527] A_12205 [528] A_12206 [529] A_12207 [530] A_12208
129 [531] A_12209 [532] A_12210 [533] A_12211 [534] A_12212 [535] A_12213
130 [536] A_12214 [537] A_12215 [538] A_12215a [539] A_12216 [540] A_12217
131 [541] A_12218 [542] A_12219 [543] A_12220 [544] A_12221 [545] A_12222
132 [546] A_12223 [547] A_12224 [548] A_12225 [549] A_12226 [550] A_12227
133 [551] A_12228 [552] A_12229 [553] A_12230 [554] A_12231 [555] A_12232
134 [556] A_12233 [557] A_12234 [558] A_12235 [559] A_12236 [560] A_12237
135 [561] A_12238 [562] A_12239 [563] A_12240 [564] A_12241 [565] A_12242
136 [566] A_12243 [567] A_12244 [568] A_12245 [569] A_12246 [570] A_12247
137 [571] A_12248 [572] A_12249 [573] A_12250 [574] A_12251 [575] A_12252
138 [576] A_12253 [577] A_12254 [578] A_12255 [579] A_12256 [580] A_12257
139 [581] A_12258 [582] A_12259 [583] A_12260 [584] A_12261 [585] A_12262
140 [586] A_12263 [587] A_12264 [588] A_12265 [589] A_12266 [590] A_12267
141 [591] A_12268 [592] A_12269 [593] A_12270 [594] A_12271 [595] A_12272
142 [596] A_12273 [597] A_12274 [598] A_12275 [599] A_12276 [600] A_12277
143 [601] A_12278 [602] A_12279 [603] A_12280 [604] A_12281 [605] A_12282
144 [606] A_12283 [607] A_12284 [608] A_12285 [609] A_12286 [610] A_12287
145 [611] A_12288 [612] A_12289 [613] A_12290 [614] A_12291 [615] A_12292
146 [616] A_12293 [617] A_12294 [618] A_12295 [619] A_12296 [620] A_12297
147 [621] A_12298 [622] A_12299 [623] A_12300 [624] A_12301 [625] A_12302
148 [626] A_12303 [627] A_12304 [628] A_12305 [629] A_12306 [630] A_12307
149 [631] A_12308 [632] A_12309 [633] A_12310 [634] A_12311 [635] A_12312
150 [636] A_12313 [637] A_12314 [638] A_12315 [639] A_12316 [640] A_12317
151 [641] A_12318 [642] A_12319 [643] A_12320 [644] A_12321 [645] A_12322
152 [646] A_12323 [647] A_12324 [648] A_12325 [649] A_12326 [650] A_12327
153 [651] A_12328 [652] A_12329 [653] A_12330 [654] A_12331 [655] A_12332
154 [656] A_12333 [657] A_12334 [658] A_12335 [659] A_12336 [660] A_12337
155 [661] A_12338 [662] A_12339 [663] A_12340 [664] A_12341 [665] A_12342
156 [666] A_12343 [667] A_12344 [668] A_12345 [669] A_12346 [670] A_12347
157 [671] A_12348 [672] A_12349 [673] A_12350 [674] A_12351 [675] A_12352
158 [676] A_12353 [677] A_12354 [678] A_12355 [679] A_12356 [680] A_12357
159 [681] A_12358 [682] A_12359 [683] A_12360 [684] A_12361 [685] A_12362
160 [686] A_12363 [687] A_12364 [688] A_12365 [689] A_12366 [690] A_12367
161 [691] A_12368 [692] A_12369 [693] A_12370 [694] A_12371 [695] A_12372
162 [696] A_12373 [697] A_12374 [698] A_12375 [699] A_12376 [700] A_12377
163 [701] A_12378 [702] A_12379 [703] A_12380 [704] A_12381 [705] A_12382
164 [706] A_12383 [707] A_12384 [708] A_12385 [709] A_12386 [710] A_12387
165 [711] A_12388 [712] A_12389 [713] A_12390 [714] A_12391 [715] A_12392
166 [716] A_12393 [717] A_12394 [718] A_12395 [719] A_12396 [720] A_12397
167 [721] A_12398 [722] A_12399 [723] A_12400 [724] A_12401 [725] A_12402
168 [726] A_12403 [727] A_12404 [728] A_12405 [729] A_12406 [730] A_12407
169 [731] A_12408 [732] A_12409 [733] A_12410 [734] A_12411 [735] A_12412
170 [736] A_12413 [737] A_12414 [738] A_12415 [739] A_12416 [740] A_12417
171 [741] A_12418 [742] A_12419 [743] A_12420 [744] A_12421 [745] A_12422
172 [746] A_12423 [747] A_12424 [748] A_12425 [749] A_12426 [750] A_12427
173 [751] A_12428 [752] A_12429 [753] A_12430 [754] A_12431 [755] A_12432
174 [756] A_12433 [757] A_12434 [758] A_12435 [759] A_12436 [760] A_12437
175 [761] A_12438 [762] A_12439 [763] A_12440 [764] A_12441 [765] A_12442
176 [766] A_12443 [767] A_12444 [768] A_12445 [769] A_12446 [770] A_12447
177 [771] A_12448 [772] A_12449 [773] A_12450 [774] A_12451 [775] A_12452
178 [776] A_12453 [777] A_12454 [778] A_12455 [779] A_12456 [780] A_12457
179 [781] A_12458 [782] A_12459 [783] A_12460 [784] A_12461 [785] A_12462
180 [786] A_12463 [787] A_12464 [788] A_12465 [789] A_12466 [790] A_12467
181 [791] A_12468 [792] A_12469 [793] A_12470 [794] A_12471 [795] A_12472
182 [796] A_12473 [797] A_12474 [798] A_12475 [799] A_12476 [800] A_12477
183 [801] A_12478 [802] A_12479 [803] A_12480 [804] A_12481 [805] A_12482
184 [806] A_12483 [807] A_12484 [808] A_12485 [809] A_12486 [810] A_12487
185 [811] A_12488 [812] A_12489 [813] A_12490 [814] A_12491 [815] A_12492
186 [816] A_12493 [817] A_12494 [818] A_12495 [819] A_12496 [820] A_12497
187 [821] A_12498 [822] A_12499 [823] A_12500 [824] A_12501 [825] A_12502
188 [826] A_12503 [827] A_12504 [828] A_12505 [829] A_12506 [830] A_12507
189 [831] A_12508 [832] A_12509 [833] A_12510 [834] A_12511 [835] A_12512
190 [836] A_12513 [837] A_12514 [838] A_12515 [839] A_12516 [840] A_12517
191 [841] A_12518 [842] A_12519 [843] A_12520 [844] A_12521 [845] A_12522
192 [846] A_12523 [847] A_12524 [848] A_12525 [849] A_12526 [850] A_12527
193 [851] A_12528 [852] A_12529 [853] A_12530 [854] A_12531 [855] A_12532
194 [856] A_12533 [857] A_12534 [858] A_12535 [859] A_12536 [860] A_12537
195 [861] A_12538 [862] A_12539 [863] A_12540 [864] A_12541 [865] A_12542
196 [866] A_12543 [867] A_12544 [868] A_12545 [869] A_12546 [870] A_12547
197 [871] A_12548 [872] A_12549 [873] A_12550 [874] A_12551 [875] A_12552
198 [876] A_12553 [877] A_12554 [878] A_12555 [879] A_12556 [880] A_12557
199 [881] A_12558 [882] A_12559 [883] A_12560 [884] A_12561 [885] A_12562
200 [886] A_12563 [887] A_12564 [888] A_12565 [889] A_12566 [890] A_12567
201 [891] A_12568 [892] A_12569 [893] A_12570 [894] A_12571 [895] A_12572
202 [896] A_12573 [897] A_12574 [898] A_12575
203 ;
205 MATRIX
207 [ 10 20 30 40 50 60 70 80 90 100]
208 [ . . . . . . . . . .]
210 Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGC [100]
211 Pan ................A.T..C.................A...............T......................T..T........C......... [100]
212 Gorilla ..................TG....T.....T........A........A......T...............................A..C.....C... [100]
213 Pongo ................AC..CC.....G..T.....T..A..C........CC....G.............................A..C.....C... [100]
214 Hylobates ......T..A..T...AC.G.C.................A..A..C..T..CC.G...........T....................A........C... [100]
215 Macaca_fuscata ......TT........AC...C..T..G.....T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T [100]
216 M._mulatta ......TT.T......AC...C.....G..T..T.....A..C..C..T..CA..TAT...........C..T........T.............AC..T [100]
217 M._fascicularis .......T........AC..CC..T.................C..C..T..CA.GTAT......T.G..C..T........T..G........T.AC..T [100]
218 M._sylvanus .......T....T...ACT..C..T...G.T.....T..A..C..C..T..CA..TAC......T.G..C....................C.....C... [100]
219 Saimiri_sciureus ................A.G..C..A........T......T....T..G..TA.G.......................T........A.T......C..A [100]
220 Tarsius_syrichta ...T....TT..A..CAC..C...T.....T.....T..C..C..C.....CC..T....T...........TA.............AGTC........A [100]
221 Lemur_catta ........TA..A...AC......A........A..T..C........A..CA..T.......T.....C.....T...........A.TC..T..C..T [100]
223 [ 110 120 130 140 150 160 170 180 190 200]
224 [ . . . . . . . . . .]
226 Homo_sapiens ATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTA [200]
227 Pan ........T.....C................................C...........C........................C.......T..C.... [200]
228 Gorilla ........T..............C.....C.................CC.............G...........C....................C.... [200]
229 Pongo ....................C.................C........CC.C.....................A.......T...C....A.....C..C. [200]
230 Hylobates ...........A....G...G..C...G.CT..........G.....C..C........CGC......................C............... [200]
231 Macaca_fuscata .C....C.A..G..C.G...........TC.....T.......C...C.........T.AAC.........TA.......T...C.............C. [200]
232 M._mulatta .C....C.A..G..C.GG..........TC.....T.......C......C......T.AAC.........TA.......T...C.............C. [200]
233 M._fascicularis .C....C.A..A..C.G...........T......T...T.G.C...C..C........CAC.........TA.......T...C............... [200]
234 M._sylvanus ......C.A..A..C.G......C....TC.............C...C..C......T.CAC.........TA....T..T..TC.....T......... [200]
235 Saimiri_sciureus .CA....CAT.TA...G...G..C.....A...T....G..T....GCC.C........C.......AT...............C.....A.AG...... [200]
236 Tarsius_syrichta .CA...GCA..AG.C.GT..C........C...T.A..T..TGC...AACA........C..C..C...T.AA.C.....G...C.T.....A..A.... [200]
237 Lemur_catta .CA...C.A..AG.A.G...GA.C.....CA.T.....T..T.....CACC........A..C..C.....AA.......A...C.....A..T....C. [200]
239 [ 210 220 230 240 250 260 270 280 290 300]
240 [ . . . . . . . . . .]
242 Homo_sapiens ACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC [300]
243 Pan .T..C..A..G........C............T.A................C............C......T...........A..........G..... [300]
244 Gorilla .......A.....G.....C..A...........A..............C.C...C..TT...........TCT.........A.T........G..... [300]
245 Pongo ....T..A...........C..A...A..G...TA.....T.....T..C.....CA.......A..................A.....A.......... [300]
246 Hylobates ....C..A..T.......TC..A...A.GG..T.C........GG....C.CT...A.TAC...C..C..G......G.....A....G........... [300]
247 Macaca_fuscata .T.....A..T.......T...AA.C.C....T.A...........CC.......CA.TA.G..A........T......T..A.T..G.....C..... [300]
248 M._mulatta .......A..T.......T...AA.C.CG...T.A........G..CC.......CA.TA..T.A......T.T.........A.T..G.....C..... [300]
249 M._fascicularis .T.....A..C.......T...AA.CAC...TT.A..T........CC.......CA.TG.GT.A..G..C..T..T......A..........C..... [300]
250 M._sylvanus .T........C.......TC..AA.C.C....T.A..T........CC.C.....CA..A....A........G.........A.T........C..... [300]
251 Saimiri_sciureus .T...G.A......T.ACTCACAA.C...T.TT.C.....T.....C..CT.T...A.TA..T.C........T..T......A.T.....A..C..... [300]
252 Tarsius_syrichta .TT..A.C..T.....G..C..AA..A..G.AG.A..T..A..G...C.CC.A...A.TA.CT.AGT...C..T....CC..TA....C........T.. [300]
253 Lemur_catta .TT..A.T..C.....A.TC..CACTA..G.AT.C.....A........C..T..AA.TA.CT.A.T...CT.A..T..G..CA....C..T..C..T.. [300]
255 [ 310 320 330 340 350 360 370 380 390 400]
256 [ . . . . . . . . . .]
258 Homo_sapiens CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACAC [400]
259 Pan .........G.................A.......................T........G....................T..T.....A..TT..... [400]
260 Gorilla ...T..T....................A...C.......A........C.C..................T.............T......A.....G... [400]
261 Pongo T.....T.....C............C.A..TA...C...A........C..............T..T........C.....T.........C........ [400]
262 Hylobates ...T..........T..T.......C.A...A....T..A...........A...............C...............TAT.A..AC.T..G... [400]
263 Macaca_fuscata T...C.......C..T.........C.A..AA.......A..T.....A.T.........G...C.C.................AT.A..A......... [400]
264 M._mulatta ....C.......C............C.A..AG.......A..T.....A.T.............C.C................TAT.A..A......... [400]
265 M._fascicularis T...C....G..C.TT...GT....C.A..AA.......A........A.T...T.........C.C................TAT.A..A......... [400]
266 M._sylvanus T..TC.......C............C.A..AG.G.....A........A.TT...........AC.T................TAT.A..AC........ [400]
267 Saimiri_sciureus A..TC.T..G.A.G..T.T.....GC.A..TC....T..AT..AG..CC.G...T........AAT...T...........T..G..A..A..T.....T [400]
268 Tarsius_syrichta ...A..T...C.A.T..T...T...C.A..AAA.TA...AT.T..T..C.....T..C.TG...C.T.....C........T..AT.A..AA........ [400]
269 Lemur_catta ......T.....A..T..T......C.A..AAA......AT.T..TTCGC.....C....C..A..C..T.................T..A.C....... [400]
271 [ 410 420 430 440 450 460 470 480 490 500]
272 [ . . . . . . . . . .]
274 Homo_sapiens CTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACA [500]
275 Pan ...........C.....T...........T..T..T.....C..T..A..CA....C........................................... [500]
276 Gorilla ...........C.......................T..T..C........CA....C.........................................T. [500]
277 Pongo ...........C......T..............AG......CG.T.....CG...AC.........................T.............A.T. [500]
278 Hylobates ..C.T....C.C.........A..........TA..........T..C...A.TC.C......C.........T........T.............A... [500]
279 Macaca_fuscata ..CG.T..A...A....T...............A.......CCTG......A....C....G............T......CT.............A..C [500]
280 M._mulatta ..CG.T..A..CA..........T.........A.......CCTG......A.T..C....G............T.......T.............A..C [500]
281 M._fascicularis ..CG.T..A...A....T.....T.........A.......CCTG......A....C.................T.......T.............A..T [500]
282 M._sylvanus ..CG.T..A...A.T..T.....T..T......A........CTA..A...A.T..C................TT.......T...C.........A..T [500]
283 Saimiri_sciureus A..A.A..A..C........TA..T.G.G....A.GG.A....TA..ACCC..AC.......T.........G.T.......T.............A.T. [500]
284 Tarsius_syrichta ....TT...T.AA....A.....TAC.......A.AG.A....TA..AACCATG.AC................A........T.........G...A.T. [500]
285 Lemur_catta A..CT....C.......AT.TA..T.A......A.A..T...CTA..ACCCA.G.AC................A-......CT............CAGA. [499]
287 [ 510 520 530 540 550 560 570 580 590 600]
288 [ . . . . . . . . . .]
290 Homo_sapiens ACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA [598]
291 Pan .........C.-.........................-T.T............T....AT.......C..G............................. [598]
292 Gorilla .........C.-.A.......................-.GT....G............A.....G..CT.G............................. [598]
293 Pongo .T..G.C.CC.-.A.......................-..................TCA.T-......G.G.................G........... [597]
294 Hylobates .T.......CG-AA...T...GC.............C-...................CTAT.......A.G............................. [598]
295 Macaca_fuscata .T....A..C.-.C...T................A..-.G....G.........C....TA...G.AC....A.TT.C..T................... [598]
296 M._mulatta .T....A....-.C...T................A..-.G.G..G.........C....TAT..G.AC....A.TT.C..T................... [598]
297 M._fascicularis .T......C..-.C..TT................A..-.G....G........TC......T..G.ACT...A.CT.C..T..C................ [598]
298 M._sylvanus .T...A.....-.C..TT................A..-TG....G..C.....TC..CA..T..G.ACT...A.CT.C..T................... [598]
299 Saimiri_sciureus .T...A.AA..-TA..TT....A............TG-.G.............T......T....A.A........T......C................ [598]
300 Tarsius_syrichta .T...A..CC.AA..TTT..........A......TA-TG.....................T....A.A......TG.........T-............ [598]
301 Lemur_catta .T...A...C.AAC-.TT.................TAATGT.T.............TGCA.T..G.A.A...A..T.C....A................. [598]
303 [ 610 620 630 640 650 660 670 680 690 700]
304 [ . . . . . . . . . .]
306 Homo_sapiens TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTC [698]
307 Pan .......C....G.......................................................T.T.....C.........T.......A...C. [698]
308 Gorilla ........................A.......................................T...T..G....C.........T..G....A..... [698]
309 Pongo ............C...........AT..................................C.G.....TTT..C..C.....TG....C...T.A..... [697]
310 Hylobates ........................A.....................................G.A...T....C..C...G...TT.....G..A..C.. [698]
311 Macaca_fuscata ................AC......AGT......CA............................T.........CC.C..C.TT.TAAC......T.TC.. [698]
312 M._mulatta ................AC......AGT.......A............................T.........CC....C.TA.TAAC......T.TC.. [698]
313 M._fascicularis ................AC......AGT......CA............................T.........CC.C..C.TA.TAAC......C.TC.. [698]
314 M._sylvanus .................C......AGT.......A............................T....T.T..CC.C..C.TA.TAAC...T..C.TC.. [698]
315 Saimiri_sciureus ..GT..T.................AG.......CA...........................---..A...TTCT.C..C..TCTAA....A..A.T.AG [695]
316 Tarsius_syrichta ..GA..TA......C.........AA..G....-A............................ATT.ATTTT.AT.CTCC.TTTTA...T.A..T..ACT [697]
317 Lemur_catta ..GA..TA.........C......AG.......-A............................ATC.ATTAT.CT..T.C...CTTG.C..A....T.AT [697]
319 [ 710 720 730 740 750 760 770 780 790 800]
320 [ . . . . . . . . . .]
322 Homo_sapiens CCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGT [798]
323 Pan .T......T.........C.........A.........................T...........G.........A....G...........C..T..C [798]
324 Gorilla .T..........T............T..A.C..T.............G...............C........T..C.................C.....C [798]
325 Pongo ......C........TACCG.T......A.......C............C..........C.........A.GGCCA........G......C......C [797]
326 Hylobates ...............TACAG.......TA.......C..T.....G....T......G..C..C......ATG.CCA.T..C..T........A.....C [798]
327 Macaca_fuscata .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C [798]
328 M._mulatta .....C..T...A..TT..G........A.C......T........CGTC.......AG....C......A.A.CC..AAT..ATG.T..C..C.....C [798]
329 M._fascicularis ...G.CC.TT..A..TT..G........ACC.....CT.T......CGT........AG.C..C......A.A.CC..AAT..ATG.T.......C.... [798]
330 M._sylvanus .....C..TT..A..TT.CG.T.....TA.C.....C.........C..CT...T..AA.C..C......A.AGCC..AAT..ATG.T..C....C...C [798]
331 Saimiri_sciureus ....C.AG.G..A.....AG.T......A...............GC.CACT......GT.C..C......CTAGCCA..ATC.A.G..C.C....C.... [795]
332 Tarsius_syrichta .T.....A....AT.TA...TT..AACAAC...AAAAT.TG...C.C.TG.......TT.C..C......AA.TC.A....C.G.G.A.....A.CA..C [797]
333 Lemur_catta .....C.TTA..T...A...TA.A.G.TACA...ATAT.......CT..C.C..TG.A.CA..C........TTC.A.T....GTG....C..C.CT..C [797]
335 [ 810 820 830 840 850 860 870 880 890 ]
336 [ . . . . . . . . . ]
338 Homo_sapiens CTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT [896]
339 Pan ..T....................A................C.........A.....G........A................................ [896]
340 Gorilla ....................TC.A................C.........A.G............A.............TT..A.............. [896]
341 Pongo ..TA....A...........T..C.......GA......ACC..CG..A.A......TG....A.A..C.....G...CTA..A.....A........ [895]
342 Hylobates ..A..T.......T.............AC..........ACC.....T..A............A.TG..........GCTAG.A.............. [896]
343 Macaca_fuscata ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.G..G......T...ATA.TG.........CTAG.C..AA.G........ [896]
344 M._mulatta ...CC.T.A.....TT.......C.T.TC.A........ACA.CC..T.GA.G......T...ATA.T..........CTAG.C..AA.A........ [896]
345 M._fascicularis ...CC.T.A.....CC.......CCT.TC.A........ACA.CC..T.G..GT.....T...ATA............TTAG.C..AA.A........ [896]
346 M._sylvanus ....CTT.A.....TT...AT..A.T.T..A........ACA..C....GA.G...G......ATA.T..........CTAAGC..AA.AT....... [896]
347 Saimiri_sciureus AC...AT.T.T..T.T.C..T..CCTTAC..G.......TCA..A..T..A............ATA..T.T......C.T.A.A..A........... [893]
348 Tarsius_syrichta ..AG....A.TGCTC.....TC.A.A.AC.A.T......A.A..C..T..C........T...ATA..G.TT..T..T.T.A.AT.A.G......... [895]
349 Lemur_catta ...A....A..T.T.T....T..C.C.TC..GA......ACA..C..T..C........T...ATA....T......CCTAA.A..A..TA.T..... [895]
350 ;
351 END;
352 BEGIN GENETICCode;
353 StandardNUCLEAR;
354 END;
356 BEGIN CODONS;
357 CODONPOSSET * UNTITLED =
358 N: 1 458-659 897 898,
359 1: 2-455\3 660-894\3,
360 2: 3-456\3 661-895\3,
361 3: 4-457\3 662-896\3;
362 CODESET * UNTITLED = mtDNA.mam: all ;
363 END;
365 BEGIN ASSUMPTIONS;
366 USERTYPE ttbias STEPMATRIX= 4
367 A C G T
368 [A] . 6 1 6
369 [C] 6 . 6 1
370 [G] 1 6 . 6
371 [T] 6 1 6 .
372 ;
374 OPTIONS DEFTYPE=unord PolyTcount=MINSTEPS ;
375 CHARSET tRNA_His = 459-528;
376 CHARSET 'tRNA_Ser_(AGY)' = 529-588;
377 CHARSET 'tRNA_Leu_(CUN)' = 589-659;
378 CHARSET noncoding = 1 458-659 897 898;
379 CHARSET position1 = 2-455\3 660-894\3;
380 CHARSET position2 = 3-456\3 661-895\3;
381 CHARSET position3 = 4-457\3 662-896\3;
382 EXSET protein_only = noncoding;
383 EXSET non_protein = position1 position2 position3;
384 EXSET only_3rds = position1 position2 noncoding;
385 EXSET only_2nds = position1 position3 noncoding;
386 EXSET only_1sts = position2 position3 noncoding;
387 END;
389 BEGIN TREES;
391 [!
392 Heuristic search settings:
394 Addition sequence: random
395 Number of replications = 10
396 Starting seed = 1
397 Global branch-swapping performed
398 MULPARS option in effect
399 Steepest descent option not in effect
400 Initial MAXTREES setting = 100
401 Branches having maximum length zero collapsed to yield polytomies
402 Trees are unrooted
403 Length of shortest tree found = 998
404 Number of trees retained = 2
405 Time used = 50.0 sec
406 ]
407 TRANSLATE
408 1 Homo_sapiens,
409 2 Pan,
410 3 Gorilla,
411 4 Pongo,
412 5 Hylobates,
413 6 Macaca_fuscata,
414 7 M._mulatta,
415 8 M._fascicularis,
416 9 M._sylvanus,
417 10 Saimiri_sciureus,
418 11 Tarsius_syrichta,
419 12 Lemur_catta
420 ;
421 TREE * 'Homo-Pan' = [&R] (12,(((((((1,2),3),4),5),(((6,7),8),9)),10),11));
422 TREE 'Pan-Gorilla' = [&R] (12,((((((1,(2,3)),4),5),(((6,7),8),9)),10),11));
423 TREE 'Homo-Gorilla' = [&R] (12,(((((((1,3),2),4),5),(((6,7),8),9)),10),11));
425 END;
429 BEGIN MACCLADE;
430 Version 3.05;
431 LastModified -1425155069;
432 Singles 0000&/0;
433 END;