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  • Committer: Bazaar Package Importer
  • Author(s): Steffen Moeller
  • Date: 2010-12-04 22:30:35 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20101204223035-j11kinhcrrdgg2p2
Tags: 1.5-1
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
  - major additions to Cookbook
  - added AlleleFreqs attribute to ensembl Variation objects.
  - added getGeneByStableId method to genome objects.
  - added Introns attribute to Transcript objects and an Intron class.
  - added Mann-Whitney test and a Monte-Carlo version
  - exploratory and confirmatory period estimation techniques (suitable for
    symbolic and continuous data)
  - Information theoretic measures (AIC and BIC) added
  - drawing of trees with collapsed nodes
  - progress display indicator support for terminal and GUI apps
  - added parser for illumina HiSeq2000 and GAiix sequence files as 
    cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
  - added parser to FASTQ files, one of the output options for illumina's
    workflow, also added cookbook demo.
  - added functionality for parsing of SFF files without the Roche tools in
    cogent.parse.binary_sff
  - thousand fold performance improvement to nmds
  - >10-fold performance improvements to some Table operations

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doc/data/Crump_example_tree_newick.txt
 
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                                        ):0.00000,
 
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111
                                      )Alcaligenaceae:0.06178,
 
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                                      (
 
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                                              ):0.00000,
 
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                                            ):0.01214
 
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                                          )Polynucleobacter:0.02121,
 
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                                        )Ralstoniaceae:0.01786,
 
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                                      ):0.01630
 
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                                    ):0.00325,
 
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                                    (
 
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                                      (
 
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                                                  (
 
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                                (
 
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                              ):0.01304,
 
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                                AF141461:0.01645
 
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                              )Methylophilales:0.06427
 
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                            ):0.00326,
 
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                            (
 
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                              AF141551:0.02426,
 
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                              AF141507:0.04615
 
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                            )Neisseriales:0.09487
 
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                          )Betaproteobacteria:0.07947,
 
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                          AF141517:0.09902
 
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                        ):0.05527,
 
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                        (
 
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                          (
 
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                            AF141532:0.01292,
 
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                            AF141542:0.00257
 
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                          ):0.00000,
 
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                          AF141424:0.00262
 
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                        )Ellin307/WD2124:0.12728
 
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                      ):0.01546
 
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                    )Gamma_beta_proteobacteria:0.02854,
 
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                    (
 
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                      (
 
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                        (
 
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                                AF141480:0.00256
 
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                              )Roseobacter:0.13561,
 
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                              (
 
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                                (
 
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                                  AF141529:0.01265,
 
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                                ):0.02966,
 
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                                  ):0.00000,
 
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                                ):0.00164
 
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                              )Rhodobacter:0.04051
 
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                            (
 
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                              AF141421:0.04514,
 
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                              AF141432:0.01539
 
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                            )Beijerinckiaceae:0.06527
 
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                          ):0.00244,
 
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                          (
 
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                              ):0.11111,
 
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                            ):0.10513,
 
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                          ):0.00653
 
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                        ):0.00487,
 
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                            AF141530:0.00000,
 
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                            AF141531:0.00000
 
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                          ):0.02863,
 
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                          AF141448:0.04585
 
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                        )Sphingomonadales:0.13392
 
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                      ):0.04010,
 
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                                            AF141598:0.00323,
 
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                                            AF141479:0.00836
 
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                                          ):0.00646,
 
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                                          AF141593:0.01564
 
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                                        ):0.01291,
 
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                                        AF141588:0.01033
 
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                                      )Pelagibacter:0.00646,
 
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                                      AF141583:0.00257
 
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                                    ):0.00000,
 
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                                    AF141539:0.00000
 
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                                  ):0.01778,
 
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                                  (
 
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                                    AF141601:0.00162,
 
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                                    AF141580:0.00769
 
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                                ):0.06022,
 
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                                (
 
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                                      AF141582:0.00000,
 
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                                      AF141585:0.00000
 
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                                    ):0.02425,
 
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                                    AF141590:0.02328
 
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                                  ):0.02274,
 
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                                  AF141395:0.04863
 
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                                ):0.00498
 
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                              )SAR11:0.04348,
 
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                              (
 
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                                AF141447:0.05616,
 
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                                (
 
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                                  AF141594:0.00256,
 
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                                  AF141584:0.00000
 
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                                ):0.06659
 
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                              ):0.02347
 
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                            ):0.00663,
 
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                            AF141567:0.22932
 
328
                          ):0.01333,
 
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                          AF141589:0.05577
 
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                        ):0.01247,
 
331
                        AF141435:0.09271
 
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                      )Consistiales:0.05054
 
333
                    )Alphaproteobacteria:0.08879
 
334
                  ):0.07221,
 
335
                  (
 
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                    (
 
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                      (
 
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                        (
 
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                          AF141472:0.16321,
 
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                          (
 
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                            AF141537:0.01302,
 
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                            AF141496:0.00838
 
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                          )Desulfobulbaceae:0.12237
 
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                        ):0.01639,
 
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                        AF141454:0.14646
 
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                      ):0.01228,
 
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                      AF141504:0.15471
 
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                    ):0.01396,
 
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                    AF141505:0.13406
 
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                  )'Delta proteobacteria':0.00581
 
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                )Proteobacteria:0.00332,
 
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                AF141560:0.18908
 
353
              ):0.00658,
 
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              (
 
355
                (
 
356
                  (
 
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                    (
 
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                      (
 
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                        (
 
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                          AF141549:0.10860,
 
361
                          (
 
362
                            (
 
363
                              (
 
364
                                (
 
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                                  (
 
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                                    (
 
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                                      (
 
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                                        (
 
369
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370
                                          AF141547:0.00258
 
371
                                        ):0.00000,
 
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                                        AF141559:0.00258
 
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                                      ):0.07190,
 
374
                                      AF141518:0.07560
 
375
                                    ):0.04246,
 
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                                    AF141474:0.07724
 
377
                                  )Cytophaga:0.01871,
 
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                                  (
 
379
                                    (
 
380
                                      (
 
381
                                        (
 
382
                                          AF141515:0.02581,
 
383
                                          (
 
384
                                            AF141519:0.02952,
 
385
                                            AF141452:0.04379
 
386
                                          ):0.01140
 
387
                                        ):0.00484,
 
388
                                        AF141451:0.02101
 
389
                                      ):0.01471,
 
390
                                      AF141466:0.06719
 
391
                                    )Sporocytophaga:0.02370,
 
392
                                    AF141524:0.04740
 
393
                                  ):0.01239
 
394
                                ):0.01304,
 
395
                                (
 
396
                                  (
 
397
                                    AF141500:0.00256,
 
398
                                    AF141552:0.00000
 
399
                                  ):0.00000,
 
400
                                  AF141502:0.00000
 
401
                                ):0.02059
 
402
                              ):0.04357,
 
403
                              AF141407:0.14560
 
404
                            ):0.03134,
 
405
                            AF141488:0.10821
 
406
                          )Flavobacteriales:0.01232
 
407
                        ):0.02462,
 
408
                        AF141543:0.10581
 
409
                      ):0.00743,
 
410
                      AF141397:0.07576
 
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                    ):0.04542,
 
412
                    (
 
413
                      (
 
414
                        AF141436:0.01862,
 
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                        AF141497:0.00325
 
416
                      ):0.00162,
 
417
                      AF141460:0.00797
 
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                    )Flexibacteraceae:0.13515
 
419
                  ):0.00494,
 
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                  (
 
421
                    AF141550:0.09051,
 
422
                    AF141418:0.03264
 
423
                  )Saprospiraceae:0.16732
 
424
                ):0.01398,
 
425
                AF141514:0.25839
 
426
              )Bacteroidetes:0.13111
 
427
            ):0.00907,
 
428
            (
 
429
              (
 
430
                (
 
431
                  (
 
432
                    AF141516:0.06810,
 
433
                    AF141562:0.03493
 
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                  )'"Planctomycetacia"':0.09418,
 
435
                  (
 
436
                    AF141399:0.00528,
 
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                    AF141417:0.00262
 
438
                  )'"Gemmatae"':0.21158
 
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                )Planctomycetes:0.09116,
 
440
                (
 
441
                  (
 
442
                    AF141391:0.02575,
 
443
                    (
 
444
                      AF141508:0.16401,
 
445
                      (
 
446
                        (
 
447
                          (
 
448
                            AF141475:0.07537,
 
449
                            AF141487:0.02921
 
450
                          ):0.02882,
 
451
                          AF141513:0.08164
 
452
                        ):0.03217,
 
453
                        AF141541:0.05472
 
454
                      ):0.02157
 
455
                    )'Verrucomicrobiae (1)':0.00906
 
456
                  ):0.03990,
 
457
                  (
 
458
                    (
 
459
                      AF141455:0.00512,
 
460
                      AF141387:0.00256
 
461
                    ):0.01132,
 
462
                    (
 
463
                      AF141408:0.00767,
 
464
                      AF141406:0.00257
 
465
                    ):0.00815
 
466
                  )'Opitutae (4)':0.18896
 
467
                )Verrucomicrobia:0.10524
 
468
              ):0.01404,
 
469
              AF141536:0.11511
 
470
            ):0.00906
 
471
          ):0.00332,
 
472
          (
 
473
            (
 
474
              (
 
475
                (
 
476
                  AF141463:0.01550,
 
477
                  AF141476:0.01081
 
478
                )'Agrococcus et al.':0.09011,
 
479
                (
 
480
                  (
 
481
                    (
 
482
                      (
 
483
                        (
 
484
                          AF141592:0.00664,
 
485
                          AF141426:0.01026
 
486
                        ):0.02268,
 
487
                        (
 
488
                          AF141402:0.01525,
 
489
                          (
 
490
                            AF141484:0.00418,
 
491
                            AF141445:0.00257
 
492
                          ):0.00486
 
493
                        ):0.00811
 
494
                      ):0.00486,
 
495
                      AF141587:0.00170
 
496
                    ):0.02354,
 
497
                    (
 
498
                      AF141442:0.00674,
 
499
                      AF141389:0.00000
 
500
                    ):0.01457
 
501
                  ):0.00489,
 
502
                  AF141411:0.06787
 
503
                )Cellulomonadaceae:0.10377
 
504
              )Actinobacteridae:0.09674,
 
505
              (
 
506
                (
 
507
                  (
 
508
                    (
 
509
                      AF141471:0.01091,
 
510
                      AF141467:0.01136
 
511
                    ):0.01798,
 
512
                    (
 
513
                      (
 
514
                        AF141400:0.00767,
 
515
                        AF141481:0.00000
 
516
                      ):0.05116,
 
517
                      (
 
518
                        AF141401:0.00512,
 
519
                        AF141433:0.00256
 
520
                      ):0.03594
 
521
                    ):0.01066
 
522
                  ):0.01065,
 
523
                  (
 
524
                    (
 
525
                      (
 
526
                        AF141522:0.00000,
 
527
                        AF141423:0.01279
 
528
                      ):0.00000,
 
529
                      AF141427:0.00000
 
530
                    ):0.00000,
 
531
                    AF141420:0.00257
 
532
                  ):0.04350
 
533
                ):0.09155,
 
534
                (
 
535
                  (
 
536
                    (
 
537
                      AF141440:0.00421,
 
538
                      AF141520:0.00256
 
539
                    ):0.00161,
 
540
                    AF141597:0.00256
 
541
                  ):0.00000,
 
542
                  AF141485:0.00256
 
543
                )'BD2-10 group':0.11726
 
544
              )Acidimicrobidae:0.04260
 
545
            )Actinobacteria:0.05311,
 
546
            (
 
547
              (
 
548
                (
 
549
                  (
 
550
                    (
 
551
                      (
 
552
                        (
 
553
                          (
 
554
                            AF141574:0.00000,
 
555
                            AF141591:0.00256
 
556
                          ):0.00000,
 
557
                          AF141579:0.00256
 
558
                        ):0.00000,
 
559
                        AF141572:0.00769
 
560
                      ):0.00000,
 
561
                      AF141565:0.00256
 
562
                    ):0.00000,
 
563
                    AF141571:0.00513
 
564
                  ):0.00000,
 
565
                  AF141575:0.00771
 
566
                ):0.00324,
 
567
                (
 
568
                  (
 
569
                    AF141596:0.00000,
 
570
                    AF141564:0.00513
 
571
                  ):0.00162,
 
572
                  (
 
573
                    AF141599:0.00256,
 
574
                    AF141578:0.01026
 
575
                  ):0.00162
 
576
                ):0.00809
 
577
              )Prochlorales:0.18823,
 
578
              (
 
579
                (
 
580
                  (
 
581
                    (
 
582
                      (
 
583
                        (
 
584
                          AF141523:0.01285,
 
585
                          AF141425:0.00258
 
586
                        ):0.00000,
 
587
                        AF141429:0.00260
 
588
                      ):0.02350,
 
589
                      AF141470:0.10407
 
590
                    ):0.00486,
 
591
                    (
 
592
                      (
 
593
                        AF141534:0.00809,
 
594
                        AF141533:0.04316
 
595
                      ):0.00647,
 
596
                      (
 
597
                        AF141412:0.00000,
 
598
                        AF141419:0.00257
 
599
                      ):0.00162
 
600
                    ):0.01456
 
601
                  ):0.04144,
 
602
                  (
 
603
                    (
 
604
                      (
 
605
                        (
 
606
                          (
 
607
                            AF141561:0.00372,
 
608
                            AF141570:0.00000
 
609
                          ):0.00000,
 
610
                          AF141576:0.00000
 
611
                        ):0.00000,
 
612
                        AF141506:0.00743
 
613
                      ):0.00000,
 
614
                      AF141573:0.00743
 
615
                    ):0.05520,
 
616
                    AF141566:0.02577
 
617
                  ):0.01571
 
618
                )'Euglena et al. chloroplasts':0.08248,
 
619
                AF141512:0.08318
 
620
              )Chloroplasts:0.03457
 
621
            )Cyanobacteria:0.16029
 
622
          ):0.00661
 
623
        ):0.01395,
 
624
        (
 
625
          AF141416:0.20329,
 
626
          AF141511:0.19093
 
627
        )'"Anaerolines"':0.09929
 
628
      ):0.00986,
 
629
      AF141540:0.22389
 
630
    ):0.03152,
 
631
    (
 
632
      AF141509:0.23520,
 
633
      (
 
634
        AF141390:0.25622,
 
635
        AF141483:0.15819
 
636
      )OP11-5:0.02369
 
637
    ):0.08699
 
638
  ):0.00913,
 
639
  (
 
640
    AF141415:0.00647,
 
641
    AF141535:0.00260
 
642
  )OP10:0.19926
 
643
)Bacteria;