File: Crump_example_tree_newick.txt

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                                      AF141563:0.00000,
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                                    AF141410:0.06022
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                                      AF141521:0.12012,
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                                    (
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                                    AF141569:0.00771
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                              (
                                AF141501:0.01323,
                                AF141528:0.00000
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                        AF141428:0.08582
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                                      (
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                                            (
                                              (
                                                (
                                                  AF141492:0.01026,
                                                  AF141453:0.00513
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                                                  AF141398:0.00000
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                                                AF141465:0.00513,
                                                AF141491:0.00256
                                              ):0.00000,
                                              AF141405:0.00256
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                                          )Polynucleobacter:0.02121,
                                          AF141431:0.03263
                                        )Ralstoniaceae:0.01786,
                                        AF141456:0.01328
                                      ):0.01630
                                    ):0.00325,
                                    (
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                                        (
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                                                (
                                                  (
                                                    AF141462:0.01064,
                                                    AF141414:0.00513
                                                  ):0.00000,
                                                  AF141457:0.00000
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                                                AF141413:0.00383
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                                              AF141459:0.08285
                                            ):0.02827,
                                            (
                                              (
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                                                  (
                                                    (
                                                      (
                                                        AF141468:0.00256,
                                                        AF141392:0.00256
                                                      ):0.00324,
                                                      AF141394:0.00000
                                                    ):0.00323,
                                                    AF141388:0.05424
                                                  ):0.01136,
                                                  AF141581:0.00998
                                                ):0.00323,
                                                (
                                                  AF141444:0.00000,
                                                  AF141446:0.00000
                                                ):0.01673
                                              ):0.02266,
                                              AF141478:0.02523
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                                          ):0.02266,
                                          AF141595:0.05097
                                        ):0.02108,
                                        (
                                          (
                                            AF141393:0.00513,
                                            AF141458:0.00256
                                          ):0.02621,
                                          AF141469:0.03147
                                        ):0.02285
                                      ):0.01541,
                                      AF141538:0.10137
                                    )Comamonadaceae:0.06378
                                  ):0.01134,
                                  AF141449:0.06970
                                )Burkholderiales:0.02283,
                                (
                                  AF141600:0.07983,
                                  AF141482:0.04023
                                ):0.00573
                              ):0.01304,
                              (
                                (
                                  (
                                    AF141486:0.00000,
                                    AF141403:0.00256
                                  ):0.00000,
                                  AF141525:0.01542
                                ):0.01546,
                                AF141461:0.01645
                              )Methylophilales:0.06427
                            ):0.00326,
                            (
                              AF141551:0.02426,
                              AF141507:0.04615
                            )Neisseriales:0.09487
                          )Betaproteobacteria:0.07947,
                          AF141517:0.09902
                        ):0.05527,
                        (
                          (
                            AF141532:0.01292,
                            AF141542:0.00257
                          ):0.00000,
                          AF141424:0.00262
                        )Ellin307/WD2124:0.12728
                      ):0.01546
                    )Gamma_beta_proteobacteria:0.02854,
                    (
                      (
                        (
                          (
                            (
                              (
                                AF141557:0.00513,
                                AF141480:0.00256
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                              (
                                (
                                  AF141529:0.01265,
                                  AF141434:0.03671
                                ):0.02966,
                                (
                                  (
                                    (
                                      AF141526:0.00256,
                                      AF141495:0.00000
                                    ):0.00000,
                                    AF141556:0.00513
                                  ):0.00000,
                                  AF141548:0.00514
                                ):0.00164
                              )Rhodobacter:0.04051
                            )Rhodobacterales:0.22265,
                            (
                              AF141421:0.04514,
                              AF141432:0.01539
                            )Beijerinckiaceae:0.06527
                          ):0.00244,
                          (
                            (
                              (
                                AF141544:0.00000,
                                AF141545:0.00000
                              ):0.11111,
                              AF141450:0.02767
                            ):0.10513,
                            AF141396:0.07575
                          ):0.00653
                        ):0.00487,
                        (
                          (
                            AF141530:0.00000,
                            AF141531:0.00000
                          ):0.02863,
                          AF141448:0.04585
                        )Sphingomonadales:0.13392
                      ):0.04010,
                      (
                        (
                          (
                            (
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                                (
                                  (
                                    (
                                      (
                                        (
                                          (
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                                            AF141479:0.00836
                                          ):0.00646,
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                                        ):0.01291,
                                        AF141588:0.01033
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                                      AF141583:0.00257
                                    ):0.00000,
                                    AF141539:0.00000
                                  ):0.01778,
                                  (
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                                  ):0.02595
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                                (
                                  (
                                    (
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                                      AF141585:0.00000
                                    ):0.02425,
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                                  ):0.02274,
                                  AF141395:0.04863
                                ):0.00498
                              )SAR11:0.04348,
                              (
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                                (
                                  AF141594:0.00256,
                                  AF141584:0.00000
                                ):0.06659
                              ):0.02347
                            ):0.00663,
                            AF141567:0.22932
                          ):0.01333,
                          AF141589:0.05577
                        ):0.01247,
                        AF141435:0.09271
                      )Consistiales:0.05054
                    )Alphaproteobacteria:0.08879
                  ):0.07221,
                  (
                    (
                      (
                        (
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                          (
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                            AF141496:0.00838
                          )Desulfobulbaceae:0.12237
                        ):0.01639,
                        AF141454:0.14646
                      ):0.01228,
                      AF141504:0.15471
                    ):0.01396,
                    AF141505:0.13406
                  )'Delta proteobacteria':0.00581
                )Proteobacteria:0.00332,
                AF141560:0.18908
              ):0.00658,
              (
                (
                  (
                    (
                      (
                        (
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                          (
                            (
                              (
                                (
                                  (
                                    (
                                      (
                                        (
                                          AF141499:0.00258,
                                          AF141547:0.00258
                                        ):0.00000,
                                        AF141559:0.00258
                                      ):0.07190,
                                      AF141518:0.07560
                                    ):0.04246,
                                    AF141474:0.07724
                                  )Cytophaga:0.01871,
                                  (
                                    (
                                      (
                                        (
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                                          (
                                            AF141519:0.02952,
                                            AF141452:0.04379
                                          ):0.01140
                                        ):0.00484,
                                        AF141451:0.02101
                                      ):0.01471,
                                      AF141466:0.06719
                                    )Sporocytophaga:0.02370,
                                    AF141524:0.04740
                                  ):0.01239
                                ):0.01304,
                                (
                                  (
                                    AF141500:0.00256,
                                    AF141552:0.00000
                                  ):0.00000,
                                  AF141502:0.00000
                                ):0.02059
                              ):0.04357,
                              AF141407:0.14560
                            ):0.03134,
                            AF141488:0.10821
                          )Flavobacteriales:0.01232
                        ):0.02462,
                        AF141543:0.10581
                      ):0.00743,
                      AF141397:0.07576
                    ):0.04542,
                    (
                      (
                        AF141436:0.01862,
                        AF141497:0.00325
                      ):0.00162,
                      AF141460:0.00797
                    )Flexibacteraceae:0.13515
                  ):0.00494,
                  (
                    AF141550:0.09051,
                    AF141418:0.03264
                  )Saprospiraceae:0.16732
                ):0.01398,
                AF141514:0.25839
              )Bacteroidetes:0.13111
            ):0.00907,
            (
              (
                (
                  (
                    AF141516:0.06810,
                    AF141562:0.03493
                  )'"Planctomycetacia"':0.09418,
                  (
                    AF141399:0.00528,
                    AF141417:0.00262
                  )'"Gemmatae"':0.21158
                )Planctomycetes:0.09116,
                (
                  (
                    AF141391:0.02575,
                    (
                      AF141508:0.16401,
                      (
                        (
                          (
                            AF141475:0.07537,
                            AF141487:0.02921
                          ):0.02882,
                          AF141513:0.08164
                        ):0.03217,
                        AF141541:0.05472
                      ):0.02157
                    )'Verrucomicrobiae (1)':0.00906
                  ):0.03990,
                  (
                    (
                      AF141455:0.00512,
                      AF141387:0.00256
                    ):0.01132,
                    (
                      AF141408:0.00767,
                      AF141406:0.00257
                    ):0.00815
                  )'Opitutae (4)':0.18896
                )Verrucomicrobia:0.10524
              ):0.01404,
              AF141536:0.11511
            ):0.00906
          ):0.00332,
          (
            (
              (
                (
                  AF141463:0.01550,
                  AF141476:0.01081
                )'Agrococcus et al.':0.09011,
                (
                  (
                    (
                      (
                        (
                          AF141592:0.00664,
                          AF141426:0.01026
                        ):0.02268,
                        (
                          AF141402:0.01525,
                          (
                            AF141484:0.00418,
                            AF141445:0.00257
                          ):0.00486
                        ):0.00811
                      ):0.00486,
                      AF141587:0.00170
                    ):0.02354,
                    (
                      AF141442:0.00674,
                      AF141389:0.00000
                    ):0.01457
                  ):0.00489,
                  AF141411:0.06787
                )Cellulomonadaceae:0.10377
              )Actinobacteridae:0.09674,
              (
                (
                  (
                    (
                      AF141471:0.01091,
                      AF141467:0.01136
                    ):0.01798,
                    (
                      (
                        AF141400:0.00767,
                        AF141481:0.00000
                      ):0.05116,
                      (
                        AF141401:0.00512,
                        AF141433:0.00256
                      ):0.03594
                    ):0.01066
                  ):0.01065,
                  (
                    (
                      (
                        AF141522:0.00000,
                        AF141423:0.01279
                      ):0.00000,
                      AF141427:0.00000
                    ):0.00000,
                    AF141420:0.00257
                  ):0.04350
                ):0.09155,
                (
                  (
                    (
                      AF141440:0.00421,
                      AF141520:0.00256
                    ):0.00161,
                    AF141597:0.00256
                  ):0.00000,
                  AF141485:0.00256
                )'BD2-10 group':0.11726
              )Acidimicrobidae:0.04260
            )Actinobacteria:0.05311,
            (
              (
                (
                  (
                    (
                      (
                        (
                          (
                            AF141574:0.00000,
                            AF141591:0.00256
                          ):0.00000,
                          AF141579:0.00256
                        ):0.00000,
                        AF141572:0.00769
                      ):0.00000,
                      AF141565:0.00256
                    ):0.00000,
                    AF141571:0.00513
                  ):0.00000,
                  AF141575:0.00771
                ):0.00324,
                (
                  (
                    AF141596:0.00000,
                    AF141564:0.00513
                  ):0.00162,
                  (
                    AF141599:0.00256,
                    AF141578:0.01026
                  ):0.00162
                ):0.00809
              )Prochlorales:0.18823,
              (
                (
                  (
                    (
                      (
                        (
                          AF141523:0.01285,
                          AF141425:0.00258
                        ):0.00000,
                        AF141429:0.00260
                      ):0.02350,
                      AF141470:0.10407
                    ):0.00486,
                    (
                      (
                        AF141534:0.00809,
                        AF141533:0.04316
                      ):0.00647,
                      (
                        AF141412:0.00000,
                        AF141419:0.00257
                      ):0.00162
                    ):0.01456
                  ):0.04144,
                  (
                    (
                      (
                        (
                          (
                            AF141561:0.00372,
                            AF141570:0.00000
                          ):0.00000,
                          AF141576:0.00000
                        ):0.00000,
                        AF141506:0.00743
                      ):0.00000,
                      AF141573:0.00743
                    ):0.05520,
                    AF141566:0.02577
                  ):0.01571
                )'Euglena et al. chloroplasts':0.08248,
                AF141512:0.08318
              )Chloroplasts:0.03457
            )Cyanobacteria:0.16029
          ):0.00661
        ):0.01395,
        (
          AF141416:0.20329,
          AF141511:0.19093
        )'"Anaerolines"':0.09929
      ):0.00986,
      AF141540:0.22389
    ):0.03152,
    (
      AF141509:0.23520,
      (
        AF141390:0.25622,
        AF141483:0.15819
      )OP11-5:0.02369
    ):0.08699
  ):0.00913,
  (
    AF141415:0.00647,
    AF141535:0.00260
  )OP10:0.19926
)Bacteria;