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Nucleic acid sequence Maximum Likelihood method, version 3.572c
Empirical Base Frequencies:
A 0.29556
C 0.19762
G 0.22984
T(U) 0.27698
Transition/transversion ratio = 2.000000
(Transition/transversion parameter = 1.537203)
User-defined trees:
+----------H.s.BLM
!
! +----------S.p.RECQ
! +----5
! ! +--------------S.c.SGS1
! !
! ! +---------H.s.RECQL
--4----3 +------6
! ! ! +------------C.e.RECQ2
! ! !
! ! ! +---------------------H.s.WRN
! +--2 +---------8
! ! ! +-------------------C.e.RECQ3
! ! +-----7
! ! ! ! +-----------E.c.RECQ
! ! ! ! +-------10
! +--1 +---9 +-------H.i.RECQ
! ! !
! ! +------------------------------B.s.RECQ
! !
! +-----------------------C.e.RECQ1
!
+--------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14638.27616
Between And Length
------- --- ------
4 H.s.BLM 0.34886
4 3 0.17455
3 5 0.16116
5 S.p.RECQ 0.35492
5 S.c.SGS1 0.47527
3 2 0.06191
2 6 0.22576
6 H.s.RECQL 0.31561
6 C.e.RECQ2 0.43697
2 1 0.06801
1 7 0.19014
7 8 0.33693
8 H.s.WRN 0.72556
8 C.e.RECQ3 0.65718
7 9 0.14273
9 10 0.30214
10 E.c.RECQ 0.38115
10 H.i.RECQ 0.23947
9 B.s.RECQ 1.01373
1 C.e.RECQ1 0.77324
4 D.m.gesta 0.49539
+----------H.s.BLM
!
! +----------S.p.RECQ
! +----5
! ! +--------------S.c.SGS1
! !
! ! +---------H.s.RECQL
--4-----3 +------6
! ! ! +------------C.e.RECQ2
! ! !
! ! ! +---------------------H.s.WRN
! +--2 +---------8
! ! ! +-------------------C.e.RECQ3
! ! +-----7
! ! ! ! +-----------E.c.RECQ
! ! ! ! +-------10
! +--1 +---9 +------H.i.RECQ
! ! !
! ! +------------------------------B.s.RECQ
! !
! +-----------------------C.e.RECQ1
!
+--------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14636.56496
Between And Length
------- --- ------
4 H.s.BLM 0.34841
4 3 0.17525
3 5 0.16012
5 S.p.RECQ 0.35466
5 S.c.SGS1 0.47349
3 2 0.06109
2 6 0.22519
6 H.s.RECQL 0.31537
6 C.e.RECQ2 0.43635
2 1 0.06713
1 7 0.18970
7 8 0.33518
8 H.s.WRN 0.72408
8 C.e.RECQ3 0.65763
7 9 0.14274
9 10 0.29966
10 E.c.RECQ 0.38152
10 H.i.RECQ 0.23901
9 B.s.RECQ 1.01001
1 C.e.RECQ1 0.77272
4 D.m.gesta 0.49348
+---------H.s.BLM
!
! +---------S.p.RECQ
! +----5
! ! +-------------S.c.SGS1
! !
! ! +---------H.s.RECQL
--4----3 +------6
! ! ! +-----------C.e.RECQ2
! ! !
! ! ! +---------------------H.s.WRN
! +--2 +---------8
! ! ! +-----------------C.e.RECQ3
! ! +-----7
! ! ! ! +---------E.c.RECQ
! ! ! ! +-------10
! +--1 +---9 +------H.i.RECQ
! ! !
! ! +---------------------------B.s.RECQ
! !
! +----------------------C.e.RECQ1
!
+-------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14600.13837
Between And Length
------- --- ------
4 H.s.BLM 0.33299
4 3 0.16388
3 5 0.14596
5 S.p.RECQ 0.33315
5 S.c.SGS1 0.45421
3 2 0.04825
2 6 0.21584
6 H.s.RECQL 0.32284
6 C.e.RECQ2 0.39228
2 1 0.06253
1 7 0.19681
7 8 0.31041
8 H.s.WRN 0.72361
8 C.e.RECQ3 0.58016
7 9 0.10544
9 10 0.28363
10 E.c.RECQ 0.32002
10 H.i.RECQ 0.24727
9 B.s.RECQ 0.92228
1 C.e.RECQ1 0.73708
4 D.m.gesta 0.44678
+---------H.s.BLM
!
! +-------H.s.RECQL
! +------5
! ! +----------C.e.RECQ2
! !
! +--4 +-----------------H.s.WRN
! ! ! +------7
! ! ! ! +--------------C.e.RECQ3
! ! +-----6
! ! ! +------E.c.RECQ
--3---2 ! +------9
! ! +--8 +-------H.i.RECQ
! ! !
! ! +----------------------B.s.RECQ
! !
! ! +-------------------C.e.RECQ1
! +--1
! ! +---------S.p.RECQ
! +--10
! +------------S.c.SGS1
!
+---------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14575.01188
Between And Length
------- --- ------
3 H.s.BLM 0.32478
3 2 0.12738
2 4 0.09269
4 5 0.21522
5 H.s.RECQL 0.26891
5 C.e.RECQ2 0.36253
4 6 0.17872
6 7 0.23295
7 H.s.WRN 0.60406
7 C.e.RECQ3 0.48597
6 8 0.10623
8 9 0.23470
9 E.c.RECQ 0.21379
9 H.i.RECQ 0.23891
8 B.s.RECQ 0.74059
2 1 0.04851
1 C.e.RECQ1 0.68189
1 10 0.12438
10 S.p.RECQ 0.32809
10 S.c.SGS1 0.41497
3 D.m.gesta 0.32045
+---------H.s.BLM
!
! +-------H.s.RECQL
! +------5
! ! +----------C.e.RECQ2
! !
! +--4 +-----------------H.s.WRN
! ! ! +------7
! ! ! ! +---------------C.e.RECQ3
! ! +-----6
! ! ! +-----E.c.RECQ
--3----2 ! +-------9
! ! +--8 +-------H.i.RECQ
! ! !
! ! +-----------------------B.s.RECQ
! !
! ! +-------------------C.e.RECQ1
! +--1
! ! +---------S.p.RECQ
! +--10
! +------------S.c.SGS1
!
+---------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14584.06309
Between And Length
------- --- ------
3 H.s.BLM 0.32589
3 2 0.14330
2 4 0.10181
4 5 0.23133
5 H.s.RECQL 0.26922
5 C.e.RECQ2 0.35517
4 6 0.18270
6 7 0.23989
7 H.s.WRN 0.59168
7 C.e.RECQ3 0.51126
6 8 0.11250
8 9 0.25298
9 E.c.RECQ 0.20823
9 H.i.RECQ 0.24987
8 B.s.RECQ 0.77749
2 1 0.06067
1 C.e.RECQ1 0.66882
1 10 0.13398
10 S.p.RECQ 0.31538
10 S.c.SGS1 0.42427
3 D.m.gesta 0.31057
+--------H.s.BLM
!
! +-------S.p.RECQ
! +---4
! ! +----------S.c.SGS1
! !
! ! +-------H.s.RECQL
--3---2 +-----5
! ! ! +---------C.e.RECQ2
! ! !
! ! ! +--------------H.s.WRN
! +--1 +---8
! ! ! +-------------C.e.RECQ3
! ! +---7
! ! ! ! +-----E.c.RECQ
! ! ! ! +-----10
! +--6 +---9 +------H.i.RECQ
! ! !
! ! +------------------B.s.RECQ
! !
! +--------------C.e.RECQ1
!
+--------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -14566.84365
Between And Length
------- --- ------
3 H.s.BLM 0.29015
3 2 0.11642
2 4 0.12675
4 S.p.RECQ 0.27215
4 S.c.SGS1 0.37416
2 1 0.07776
1 5 0.19102
5 H.s.RECQL 0.26723
5 C.e.RECQ2 0.31502
1 6 0.09837
6 7 0.14774
7 8 0.13342
8 H.s.WRN 0.49443
8 C.e.RECQ3 0.44128
7 9 0.11415
9 10 0.22308
10 E.c.RECQ 0.19340
10 H.i.RECQ 0.23928
9 B.s.RECQ 0.62976
6 C.e.RECQ1 0.50705
3 D.m.gesta 0.28996
+---------H.s.BLM
!
! +---------H.s.RECQL
! +-----4
! ! +------------C.e.RECQ2
! !
! ! +---------------------H.s.WRN
! +--3 +---------7
! ! ! +---6 +-------------------C.e.RECQ3
! ! ! ! !
! ! ! ! +-------------------C.e.RECQ1
! ! +--5
! ! ! +-----------E.c.RECQ
--1-----2 ! +--------9
! ! +--------8 +------H.i.RECQ
! ! !
! ! +------------------------------B.s.RECQ
! !
! ! +----------S.p.RECQ
! +---10
! +-------------S.c.SGS1
!
+--------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15121.03186
Between And Length
------- --- ------
1 H.s.BLM 0.51465
1 2 0.28090
2 3 0.10315
3 4 0.32082
4 H.s.RECQL 0.49293
4 C.e.RECQ2 0.65860
3 5 0.15456
5 6 0.17474
6 7 0.52689
7 H.s.WRN 1.09334
7 C.e.RECQ3 1.00705
6 C.e.RECQ1 1.02232
5 8 0.43664
8 9 0.44492
9 E.c.RECQ 0.59316
9 H.i.RECQ 0.34921
8 B.s.RECQ 1.55804
2 10 0.24197
10 S.p.RECQ 0.53780
10 S.c.SGS1 0.71586
1 D.m.gesta 0.77117
+----------H.s.BLM
!
! +---------H.s.RECQL
! +------5
! ! +------------C.e.RECQ2
! !
! +--4 +---------------------------H.s.WRN
! ! ! +----7
! ! ! ! ! +------------------------C.e.RECQ3
! ! ! ! +--8
! ! +-------6 +-------------------------------B.s.RECQ
! +--3 !
! ! ! ! +------------E.c.RECQ
! ! ! +------------9
! ! ! +-----H.i.RECQ
--1-----2 !
! ! +------------------------C.e.RECQ1
! !
! ! +----------S.p.RECQ
! +---10
! +-------------S.c.SGS1
!
+--------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15159.46281
Between And Length
------- --- ------
1 H.s.BLM 0.52954
1 2 0.28932
2 3 0.08298
3 4 0.04876
4 5 0.32499
5 H.s.RECQL 0.50305
5 C.e.RECQ2 0.66125
4 6 0.37898
6 7 0.23694
7 H.s.WRN 1.37337
7 8 0.02671
8 C.e.RECQ3 1.26945
8 B.s.RECQ 1.62440
6 9 0.63154
9 E.c.RECQ 0.64636
9 H.i.RECQ 0.30582
3 C.e.RECQ1 1.25364
2 10 0.24695
10 S.p.RECQ 0.54591
10 S.c.SGS1 0.71830
1 D.m.gesta 0.77333
+-------------H.s.BLM
+--4
! ! +----------S.p.RECQ
+--3 +-----5
! ! +--------------S.c.SGS1
! !
+--2 +-------------------------C.e.RECQ1
! !
! ! +---------H.s.RECQL
! +-------6
! +-------------C.e.RECQ2
!
! +----------------------------H.s.WRN
! +-----8
! ! ! +------------------------C.e.RECQ3
! ! +--9
--1-------7 +--------------------------------B.s.RECQ
! !
! ! +------------E.c.RECQ
! +-----------10
! +-----H.i.RECQ
!
+-----------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15218.49216
Between And Length
------- --- ------
1 2 0.05072
2 3 0.01508
3 4 0.05828
4 H.s.BLM 0.70110
4 5 0.29103
5 S.p.RECQ 0.55246
5 S.c.SGS1 0.73834
3 C.e.RECQ1 1.32136
2 6 0.40618
6 H.s.RECQL 0.51741
6 C.e.RECQ2 0.67532
1 7 0.40663
7 8 0.28484
8 H.s.WRN 1.43023
8 9 0.00506
9 C.e.RECQ3 1.26407
9 B.s.RECQ 1.64155
7 10 0.63718
10 E.c.RECQ 0.64505
10 H.i.RECQ 0.31975
1 D.m.gesta 0.91821
+-------------H.s.BLM
+--4
! +-------------------------C.e.RECQ1
+--3
! ! +----------S.p.RECQ
! +-----5
+--2 +--------------S.c.SGS1
! !
! ! +---------H.s.RECQL
! +-------6
! +------------C.e.RECQ2
!
! +----------------------------H.s.WRN
! +----8
! ! ! +------------------------C.e.RECQ3
! ! +--9
--1-------7 +--------------------------------B.s.RECQ
! !
! ! +------------E.c.RECQ
! +-----------10
! +-----H.i.RECQ
!
+-----------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15215.34414
Between And Length
------- --- ------
1 2 0.05053
2 3 0.03355
3 4 0.03112
4 H.s.BLM 0.69687
4 C.e.RECQ1 1.30505
3 5 0.30808
5 S.p.RECQ 0.55385
5 S.c.SGS1 0.73382
2 6 0.41071
6 H.s.RECQL 0.51752
6 C.e.RECQ2 0.67494
1 7 0.40981
7 8 0.26890
8 H.s.WRN 1.44075
8 9 0.00729
9 C.e.RECQ3 1.27137
9 B.s.RECQ 1.63422
7 10 0.64002
10 E.c.RECQ 0.64500
10 H.i.RECQ 0.31795
1 D.m.gesta 0.91484
+-------------H.s.BLM
+--4
! ! +----------S.p.RECQ
+--3 +-----5
! ! +--------------S.c.SGS1
! !
+--2 +--------------------------C.e.RECQ1
! !
! ! +---------H.s.RECQL
! +-------6
! +------------C.e.RECQ2
!
! +-----------------------H.s.WRN
! +----------9
! +--8 +-------------------C.e.RECQ3
! ! !
--1-------7 +-------------------------------B.s.RECQ
! !
! ! +------------E.c.RECQ
! +----------10
! +------H.i.RECQ
!
+-----------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15224.51495
Between And Length
------- --- ------
1 2 0.05186
2 3 0.03357
3 4 0.04529
4 H.s.BLM 0.70750
4 5 0.29400
5 S.p.RECQ 0.56194
5 S.c.SGS1 0.74070
3 C.e.RECQ1 1.33583
2 6 0.41262
6 H.s.RECQL 0.52563
6 C.e.RECQ2 0.67698
1 7 0.42025
7 8 0.13936
8 9 0.54017
9 H.s.WRN 1.20281
9 C.e.RECQ3 0.99889
8 B.s.RECQ 1.59185
7 10 0.61311
10 E.c.RECQ 0.63958
10 H.i.RECQ 0.33359
1 D.m.gesta 0.91870
+-------------H.s.BLM
+--4
! ! +----------S.p.RECQ
+--3 +-----5
! ! +--------------S.c.SGS1
! !
+--2 +-------------------------C.e.RECQ1
! !
! ! +----------H.s.RECQL
! +-------6
! +------------C.e.RECQ2
!
! +-------------------------------H.s.WRN
! +--8
! ! ! +------------E.c.RECQ
! ! +-----------9
--1--------7 +-----H.i.RECQ
! !
! ! +--------------------------C.e.RECQ3
! +-10
! +-------------------------------B.s.RECQ
!
+-----------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15214.36850
Between And Length
------- --- ------
1 2 0.04106
2 3 0.02878
3 4 0.01965
4 H.s.BLM 0.70518
4 5 0.29987
5 S.p.RECQ 0.55536
5 S.c.SGS1 0.73157
3 C.e.RECQ1 1.31481
2 6 0.41610
6 H.s.RECQL 0.51834
6 C.e.RECQ2 0.66773
1 7 0.43709
7 8 0.05912
8 H.s.WRN 1.58522
8 9 0.62659
9 E.c.RECQ 0.64483
9 H.i.RECQ 0.31441
7 10 0.14384
10 C.e.RECQ3 1.34076
10 B.s.RECQ 1.57785
1 D.m.gesta 0.92294
+-------------H.s.BLM
+--4
! +-------------------------C.e.RECQ1
+--3
! ! +----------S.p.RECQ
! +-----5
+--2 +--------------S.c.SGS1
! !
! ! +----------H.s.RECQL
! +-------6
! +-------------C.e.RECQ2
!
! +-----------------------H.s.WRN
! +----------9
! +--8 +-------------------C.e.RECQ3
! ! !
--1-------7 +-------------------------------B.s.RECQ
! !
! ! +------------E.c.RECQ
! +----------10
! +------H.i.RECQ
!
+-----------------D.m.gesta
remember: (although rooted by outgroup) this is an unrooted tree!
Ln Likelihood = -15222.97107
Between And Length
------- --- ------
1 2 0.05192
2 3 0.04479
3 4 0.03127
4 H.s.BLM 0.69902
4 C.e.RECQ1 1.32194
3 5 0.30691
5 S.p.RECQ 0.56334
5 S.c.SGS1 0.73764
2 6 0.41740
6 H.s.RECQL 0.52537
6 C.e.RECQ2 0.67766
1 7 0.42347
7 8 0.12338
8 9 0.54978
9 H.s.WRN 1.20376
9 C.e.RECQ3 1.00000
8 B.s.RECQ 1.59806
7 10 0.61680
10 E.c.RECQ 0.63939
10 H.i.RECQ 0.33286
1 D.m.gesta 0.91766
Tree Ln L Diff Ln L Its S.D. Significantly worse?
1-14638.27616 -71.43251 32.0178 Yes
2-14636.56496 -69.72131 31.8184 Yes
3-14600.13837 -33.29472 25.3242 No
4-14575.01188 -8.16823 13.8003 No
5-14584.06309 -17.21944 15.3130 No
6-14566.84365 <------ best
7-15121.03186 -554.18821 71.8056 Yes
8-15159.46281 -592.61916 73.8815 Yes
9-15218.49216 -651.64851 76.6188 Yes
10-15215.34414 -648.50049 76.5595 Yes
11-15224.51495 -657.67130 76.6822 Yes
12-15214.36850 -647.52485 76.6792 Yes
13-15222.97107 -656.12743 76.6873 Yes