Knowledge

Archaeopteryx (software)

Source 📝

87: 705: 693: 628: 17: 623: 193:. Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), it also implements the 665: 350: 107: 731: 697: 643: 671: 66: 587: 170: 50: 677: 139: 633: 478: 410: 618: 490: 318: 659: 575: 378: 343: 638: 592: 398: 383: 174: 8: 608: 582: 440: 427: 388: 86: 562: 373: 246: 219: 287: 270: 613: 422: 336: 292: 251: 178: 166: 537: 532: 282: 241: 231: 123: 97: 552: 542: 527: 463: 709: 547: 450: 393: 112: 725: 522: 468: 432: 236: 190: 116: 629:
Matrix-assisted laser desorption ionization-time of flight mass spectrometer
512: 473: 405: 296: 255: 323: 485: 417: 570: 517: 507: 502: 182: 75: 36: 497: 359: 194: 186: 319:
List of phylogeny software, hosted at the University of Washington
458: 220:"phyloXML: XML for evolutionary biology and comparative genomics" 271:"ATV: display and manipulation of annotated phylogenetic trees" 18:
Archaeopteryx (evolutionary tree visualization and analysis)
328: 128: 313: 217: 197:
format. Archaeopteryx is the successor to Java program
181:. This type of program can be used for a variety of 268: 723: 344: 269:Zmasek, Christian M.; Eddy, Sean R. (2001). 624:Matrix-assisted laser desorption ionization 218:Han, Mira V.; Zmasek, Christian M. (2009). 692: 351: 337: 85: 286: 245: 235: 14: 724: 27:Phylogenetic tree analyzation software 666:European Molecular Biology Laboratory 332: 189:, but is particularly designed for 24: 25: 743: 307: 704: 703: 691: 644:Chromosome conformation capture 288:10.1093/bioinformatics/17.4.383 262: 211: 56:0.972+ beta 9M / 2012.08.08 13: 1: 672:National Institutes of Health 204: 358: 7: 588:Structure-based drug design 10: 748: 687: 678:Wellcome Sanger Institute 652: 601: 561: 449: 366: 177:, editing, and analyzing 134: 122: 106: 96: 65: 61: 49: 45: 35: 634:Microfluidic-based tools 479:Human Connectome Project 411:Human Microbiome Project 237:10.1186/1471-2105-10-356 102:Windows, Linux, Mac OS X 619:Electrospray ionization 491:Human Epigenome Project 732:Phylogenetics software 660:DNA Data Bank of Japan 576:Human proteome project 379:Computational genomics 639:Isotope affinity tags 593:Expression proteomics 399:Human Genome Project 384:Comparative genomics 169:program, written in 609:2-D electrophoresis 583:Call-map proteomics 441:Structural genomics 428:Population genomics 389:Functional genomics 187:molecular data sets 41:Christian M. Zmasek 32: 563:Structural biology 374:Cognitive genomics 224:BMC Bioinformatics 179:phylogenetic trees 165:is an interactive 30: 719: 718: 614:Mass spectrometer 423:Personal genomics 167:computer software 160: 159: 16:(Redirected from 739: 707: 706: 695: 694: 538:Pharmacogenomics 533:Pharmacogenetics 353: 346: 339: 330: 329: 301: 300: 290: 266: 260: 259: 249: 239: 215: 156: 153: 151: 149: 147: 145: 143: 141: 98:Operating system 89: 84: 81: 79: 77: 33: 29: 21: 747: 746: 742: 741: 740: 738: 737: 736: 722: 721: 720: 715: 683: 648: 597: 557: 553:Transcriptomics 543:Systems biology 528:Paleopolyploidy 464:Cheminformatics 445: 362: 357: 310: 305: 304: 267: 263: 216: 212: 207: 138: 92: 74: 57: 28: 23: 22: 15: 12: 11: 5: 745: 735: 734: 717: 716: 714: 713: 701: 688: 685: 684: 682: 681: 675: 669: 663: 656: 654: 650: 649: 647: 646: 641: 636: 631: 626: 621: 616: 611: 605: 603: 602:Research tools 599: 598: 596: 595: 590: 585: 580: 579: 578: 567: 565: 559: 558: 556: 555: 550: 548:Toxicogenomics 545: 540: 535: 530: 525: 520: 515: 510: 505: 500: 495: 494: 493: 483: 482: 481: 471: 466: 461: 455: 453: 451:Bioinformatics 447: 446: 444: 443: 438: 430: 425: 420: 415: 414: 413: 403: 402: 401: 394:Genome project 391: 386: 381: 376: 370: 368: 364: 363: 356: 355: 348: 341: 333: 327: 326: 321: 316: 309: 308:External links 306: 303: 302: 281:(4): 383–384. 275:Bioinformatics 261: 209: 208: 206: 203: 158: 157: 154:/archaeopteryx 136: 132: 131: 126: 120: 119: 113:Bioinformatics 110: 104: 103: 100: 94: 93: 91: 90: 71: 69: 63: 62: 59: 58: 55: 53: 51:Stable release 47: 46: 43: 42: 39: 26: 9: 6: 4: 3: 2: 744: 733: 730: 729: 727: 712: 711: 702: 700: 699: 690: 689: 686: 679: 676: 673: 670: 667: 664: 661: 658: 657: 655: 653:Organizations 651: 645: 642: 640: 637: 635: 632: 630: 627: 625: 622: 620: 617: 615: 612: 610: 607: 606: 604: 600: 594: 591: 589: 586: 584: 581: 577: 574: 573: 572: 569: 568: 566: 564: 560: 554: 551: 549: 546: 544: 541: 539: 536: 534: 531: 529: 526: 524: 523:Nutrigenomics 521: 519: 516: 514: 511: 509: 506: 504: 501: 499: 496: 492: 489: 488: 487: 484: 480: 477: 476: 475: 472: 470: 469:Chemogenomics 467: 465: 462: 460: 457: 456: 454: 452: 448: 442: 439: 437: 435: 431: 429: 426: 424: 421: 419: 416: 412: 409: 408: 407: 404: 400: 397: 396: 395: 392: 390: 387: 385: 382: 380: 377: 375: 372: 371: 369: 365: 361: 354: 349: 347: 342: 340: 335: 334: 331: 325: 324:Archaeopteryx 322: 320: 317: 315: 312: 311: 298: 294: 289: 284: 280: 276: 272: 265: 257: 253: 248: 243: 238: 233: 229: 225: 221: 214: 210: 202: 200: 199:A Tree Viewer 196: 192: 191:phylogenomics 188: 184: 180: 176: 172: 168: 164: 163:Archaeopteryx 155: 137: 133: 130: 127: 125: 121: 118: 117:phylogenomics 114: 111: 109: 105: 101: 99: 95: 88: 83: 73: 72: 70: 68: 64: 60: 54: 52: 48: 44: 40: 38: 34: 31:Archaeopteryx 19: 708: 696: 518:Microbiomics 513:Metabolomics 474:Connectomics 433: 406:Metagenomics 278: 274: 264: 227: 223: 213: 198: 162: 161: 37:Developer(s) 486:Epigenomics 418:Pangenomics 571:Proteomics 508:Lipidomics 503:Immunomics 205:References 67:Repository 498:Glycomics 152:/software 148:/cmzmasek 82:/forester 80:/cmzmasek 726:Category 710:Category 436:genomics 360:Genomics 314:phyloXML 297:11301314 256:19860910 195:phyloXML 183:analyses 459:Biochip 247:2774328 230:: 356. 201:(ATV). 175:viewing 142:.google 135:Website 124:License 367:Fields 295:  254:  244:  173:, for 76:github 674:(USA) 434:Socio 150:/home 146:/site 140:sites 698:List 680:(UK) 668:(EU) 662:(JP) 293:PMID 252:PMID 171:Java 144:.com 129:LGPL 108:Type 78:.com 283:doi 242:PMC 232:doi 185:of 728:: 291:. 279:17 277:. 273:. 250:. 240:. 228:10 226:. 222:. 115:, 352:e 345:t 338:v 299:. 285:: 258:. 234:: 20:)

Index

Archaeopteryx (evolutionary tree visualization and analysis)
Developer(s)
Stable release
Repository
github.com/cmzmasek/forester
Edit this at Wikidata
Operating system
Type
Bioinformatics
phylogenomics
License
LGPL
sites.google.com/site/cmzmasek/home/software/archaeopteryx
computer software
Java
viewing
phylogenetic trees
analyses
molecular data sets
phylogenomics
phyloXML
"phyloXML: XML for evolutionary biology and comparative genomics"
doi
10.1186/1471-2105-10-356
PMC
2774328
PMID
19860910
"ATV: display and manipulation of annotated phylogenetic trees"
doi

Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.