I need distances from root to the all branches. When I use simple tree (Y:2,((F:5,M:3)B:2)A:1 for example) then commands
library(ape) tree <- read.tree (file.choose()) dist.nodes(tree)[, Ntip(tree) + 1] gives correct result (2 8 6 0 1 3 ). But when I use long tree (it is in the end of this letter, it is dinosaurs tree from paper http://www.graemetlloyd.com/matrdino.html) it give wrong result: "1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 NA NA NA NA NA NA NA NA NA NA NA ..." Why it is? Tree: (A1:1,((A2:292,(A3:129,(A4:206,((A5:337,(A6:127,(A7:335,((A8:174,(A9:276,(A1 0:91,(A11:87,((A12:405,(A13:101,A14:169)),(A15:392,((A16:196,A17:208),(A18:3 57,A19:358)))))))),(A20:363,(A21:175,((A22:176,(A23:76,(A24:283,(A25:331,(A2 6:345,(A27:273,(A28:119,A29:120))))))),(A30:146,(A31:28,(A32:234,((A33:242,( A34:150,A35:298)),(A36:153,(A37:340,((A38:380,A39:389),((A40:370,(A41:290,A4 2:291)),(A43:254,((A44:29,A45:138),(A46:326,A47:372)))))))))))))))))),(A48:3 61,(((A49:3,A50:170),((A51:359,(A52:404,(A53:413,(A54:158,(A55:172,(A56:262, (A57:356,((A58:118,(A59:302,A60:394)),((A61:270,A62:364),((A63:299,A64:300), (A65:301,A66:352))))))))))),(A67:414,(A68:312,((A69:81,A70:409),((A71:313,A7 2:314),(A73:209,(A74:410,(A75:39,((A76:239,(A77:310,(A78:303,(A79:205,A80:39 7)))),((A81:53,(A82:159,A83:309)),(A84:420,(A85:50,((A86:236,((A87:365,(A88: 77,A:78)),(A89:124,(A90:4,(A91:271,A92:272))))),(((A93:25,A94:45),(A95:386,( A96:106,A97:384))),(A98:84,(A99:287,(A100:85,(A101:83,A102:86))))))))))))))) )))),(A103:10,(A104:171,((A105:267,A106:411),((A107:266,A108:419),(A109:190, (A110:179,(A111:149,(A112:279,(A113:379,(A114:376,(A115:377,(A116:241,((A117 :321,(A118:416,A119:417)),((A120:114,A121:115),(A122:71,(A123:218,(A124:134, (A125:181,(A126:180,(A127:268,(A128:144,(A129:17,(A130:246,(A131:193,(A132:3 04,(A133:130,(A134:311,(A135:52,((A136:152,A137:375),(A138:142,((A139:214,(( A140:160,(A141:65,A142:220)),((A143:121,A144:122),(A145:197,(A146:307,(A147: 243,(A148:200,A149:330))))))),(A150:277,(A151:390,(A152:189,(A153:24,((A154: 82,A155:278),((A156:201,A157:202),(A158:98,(A159:258,(A160:178,(A161:177,A16 2:252))))))))))))))))))))))))))))))))))))))))))))))),((A163:329,((A164:274,A 165:378),(A166:240,(A167:192,(A168:123,((A169:21,(A170:323,(((A171:164,A172: 217),(A173:227,A174:415)),(A175:295,(A176:293,(A177:95,(A178:294,A179:398))) )))),(A180:26,((A181:231,(A182:70,A183:207)),(A184:62,(A185:32,(A186:156,(A1 87:186,(A188:373,(A189:199,(A190:403,(A200:342,(A201:57,((A202:224,(A203:259 ,A204:260)),(A205:282,(A206:80,((A207:215,A208:418),(A209:194,(A210:166,((A2 11:23,((A212:212,(A213:251,A214:319,A215:320)),((A216:367,(A217:19,(A218:66, A219:107))),((A220:110,(A221:383,(A222:58,A223:111))),(A224:35,(A225:37,(A22 6:33,A227:34,A228:36))))))),((A229:46,A230:165),(A231:69,(A232:20,(A233:64,( (A234:139,(A235:204,(A236:63,A237:75))),((A238:103,(A239:137,A240:374)),((A2 41:31,(A242:315,(A243:248,A244:318))),(A245:61,(A246:288,(A247:27,(A248:296, (A249:22,(A250:11,(A251:275,(A252:133,(A253:49,(A254:223,(A255:155,(A256:187 ,(A257:381,((A258:12,A259:286),((A260:43,(A261:324,(A262:188,(A263:222,A264: 327)))),(A265:8,(A266:382,(A267:42,(A268:261,(A269:213,A270:284))))))))))))) )))))))))))))))))))))))))))))))))))))),((A271:355,(A272:89,A273:168)),(A274: 131,(A275:161,(((A276:328,A277:421),(A278:109,(A279:154,((A280:210,A281:211) ,(A282:306,(A283:368,(A284:93,A285:338))))))),((A286:126,((A287:79,A288:354) ,(A289:402,(A290:406,(A291:325,((A292:226,A293:253),(A294:182,(A295:2,((A296 :48,A297:73),(A298:55,A299:203,A300:221)))))))))),(A301:369,((((A302:9,A303: 289),(A304:228,A305:297)),((A306:385,(A307:117,A308:140)),(A309:229,(A310:88 ,(A311:99,((A312:59,A313:366),(A314:185,A315:353))))))),((A316:216,(A317:237 ,(A318:100,((A319:351,A320:412),(A321:16,(A322:249,(A323:6,(A324:396,(A325:7 2,(A326:151,A327:225)))))))))),(A328:143,(A329:391,(A330:219,((A331:344,((A3 32:108,(A333:162,(A334:116,A335:360))),(A336:132,(A337:14,(A338:15,((A339:13 ,A340:157),(A341:38,((A342:102,A343:393),(A344:395,(A345:244,A346:371))))))) ))),((A347:257,(A348:148,(A349:247,(A350:173,(A351:349,(A352:44,(A353:96,A35 4:235))))))),(A355:336,((A356:408,(A357:305,(A358:105,A359:263))),(A360:94,( (A361:285,(A362:341,(A363:167,(A364:147,(A365:41,(A366:347,((A367:30,A368:14 5),(A369:362,(A370:264,A371:265))))))))),((A372:54,A373:407),((A374:316,((A3 75:245,(A376:141,(A377:256,(A378:60,(A379:128,(A380:136,(A381:135,A382:339)) ))))),(A383:183,((A384:74,A385:125),(A386:51,((A387:90,A388:255),(A389:233,( (A390:322,(A391:92,A392:195)),(A393:198,(A394:269,(A395:97,A396:184))))))))) )),((A397:18,(A398:281,(A399:343,(A400:238,A401:280)))),(A402:163,(A403:308, ((A404:399,(A405:317,(A406:40,A407:191))),(((A408:230,A409:350),(A410:112,(A 411:346,(A412:68,(A413:387,(A414:332,A415:333)))))),(A416:250,(A417:232,(A41 8:348,(A419:67,((A420:7,(A421:5,(A422:113,A423:400))),(A424:334,((A425:388,A 426:401),(A427:56,(A428:47,A429:104)))))))))))))))))))))))))))))))))))); _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
