PUZZLE 4.0.2
Type of analysis: tree reconstruction
Parameter estimation: approximate (faster)
Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation)
Standard errors (S.E.) are obtained by the curvature method.
The upper and lower bounds of an approximate 95% confidence interval
for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E.
SEQUENCE ALIGNMENT
Input data: 34 sequences with 1507 amino acid sites
Number of constant sites: 14 (= 0.9% of all sites)
SUBSTITUTION PROCESS
Model of substitution: JTT (Jones et al. 1992)
Amino acid frequencies (estimated from data set):
pi(A) = 6.3%
pi(R) = 5.3%
pi(N) = 4.2%
pi(D) = 6.2%
pi(C) = 1.4%
pi(Q) = 2.9%
pi(E) = 8.2%
pi(G) = 5.7%
pi(H) = 2.3%
pi(I) = 6.2%
pi(L) = 9.0%
pi(K) = 7.4%
pi(M) = 1.8%
pi(F) = 4.5%
pi(P) = 4.4%
pi(S) = 5.4%
pi(T) = 4.9%
pi(W) = 2.4%
pi(Y) = 4.2%
pi(V) = 7.4%
RATE HETEROGENEITY
Model of rate heterogeneity: uniform rate
SEQUENCES IN INPUT ORDER
5% chi-square test p-value
Pyrococcus failed 0.00% [82]
Methanococ failed 0.00% [99]
METHANOBAC failed 0.00% [50]
Archaeoglo failed 0.00% [102]
Sulfolobus passed 23.91% [146]
Arabidopsi passed 28.84% [151]
Tetrahymen failed 3.10% [136]
Homosapien failed 3.72% [132]
Celegans passed 23.63% [111]
Saccharomy passed 46.46% [126]
Schizosacc passed 99.80% [111]
Nosema failed 0.19% [175]
Chlamydia passed 78.86% [157]
Chlamydoph passed 83.32% [133]
Borrelia failed 0.00% [145]
Treponema failed 0.00% [171]
Mycobacter failed 0.00% [146]
Rickettsia failed 0.02% [160]
Staphyloco failed 0.00% [138]
Thermus failed 0.00% [154]
Helicobact failed 0.05% [184]
Campylobac failed 0.08% [183]
Haemophilu passed 87.24% [138]
Ecoli failed 0.00% [132]
Pseudomona failed 1.17% [130]
Streptococ passed 28.91% [141]
Bacillus passed 95.53% [128]
Fervidobac passed 53.76% [131]
Thermotoga failed 2.84% [182]
Aquifex failed 0.41% [190]
Ciona passed 6.88% [389]
Synechocys failed 0.67% [120]
Mycoplasma failed 0.00% [125]
Deinococcu failed 0.00% [430]
The chi-square tests compares the amino acid composition of each sequence
to the frequency distribution assumed in the maximum likelihood model.
The number in square brackets indicates how often each sequence is
involved in one of the 1307 completely unresolved quartets of the
quartet puzzling tree search.
IDENTICAL SEQUENCES
The sequences in each of the following groups are all identical. To speed
up computation please remove all but one of each group from the data set.
All sequences are unique.
MAXIMUM LIKELIHOOD DISTANCES
Maximum likelihood distances are computed using the selected model of
substitution and rate heterogeneity.
34
Pyrococcus 0.00000 0.82650 0.83797 0.89302 0.94910 1.75726 1.85327
1.74888 1.76125 1.68309 1.72183 1.62609 1.62444 1.59652
1.49644 1.64214 1.54037 1.75741 1.43751 1.18206 1.99893
1.99646 1.85262 2.06623 2.00965 1.92417 1.72876 1.61218
1.69248 1.76808 1.99694 2.05394 1.91974 1.93543
Methanococ 0.82650 0.00000 0.85911 1.00647 1.00445 1.84511 1.82556
1.75320 1.75264 1.66618 1.74112 1.58566 1.68293 1.71314
1.58563 1.78505 1.77980 1.74480 1.58626 1.31069 1.96993
1.95403 1.73718 1.88188 1.92141 1.87592 1.73715 1.59416
1.64019 1.73082 1.89911 1.95529 1.90691 1.87108
METHANOBAC 0.83797 0.85911 0.00000 0.79584 0.96717 1.76096 1.78763
1.69463 1.79666 1.67357 1.66841 1.49526 1.56123 1.57282
1.50145 1.64148 1.61629 1.68327 1.51189 1.16658 1.98418
2.06993 1.75694 1.96486 1.82155 1.78722 1.60983 1.57294
1.63334 1.82259 1.99856 1.95102 1.74035 2.04272
Archaeoglo 0.89302 1.00647 0.79584 0.00000 0.92645 1.76368 1.80584
1.80021 1.83984 1.71432 1.74593 1.54715 1.62377 1.64810
1.59895 1.75406 1.71761 1.80690 1.50418 1.30447 1.95829
1.93790 1.68421 1.83541 1.82664 1.79848 1.62450 1.61501
1.60683 1.71517 1.94878 1.98014 1.98560 1.93796
Sulfolobus 0.94910 1.00445 0.96717 0.92645 0.00000 1.57440 1.43425
1.49564 1.56561 1.51343 1.57107 1.60786 1.68523 1.59856
1.47444 1.62763 1.60691 1.71063 1.36242 1.42564 1.59044
1.62586 1.32535 1.48817 1.66060 1.50741 1.41627 1.34472
1.31330 1.42109 1.76315 1.53957 1.81201 2.21132
Arabidopsi 1.75726 1.84511 1.76096 1.76368 1.57440 0.00000 0.82622
0.91491 0.93929 0.84401 0.83309 0.93571 1.06893 1.11156
1.14439 1.21164 1.26524 1.30757 1.52960 1.27792 2.28496
2.27071 2.06482 2.27591 2.11580 2.09505 1.99590 1.99116
2.03108 2.03213 2.22733 2.31224 2.09318 1.62996
Tetrahymen 1.85327 1.82556 1.78763 1.80584 1.43425 0.82622 0.00000
0.83897 0.92102 0.91222 0.86726 0.92873 1.18796 1.22325
1.14487 1.35315 1.35543 1.34877 1.50476 1.33845 2.27132
2.28403 2.16368 2.23306 2.20921 2.04114 2.06201 2.04307
2.09193 2.11774 2.17370 2.37390 2.16557 1.76102
Homosapien 1.74888 1.75320 1.69463 1.80021 1.49564 0.91491 0.83897
0.00000 0.68977 0.76977 0.72571 0.82487 1.05110 1.08427
1.11446 1.21505 1.22727 1.29788 1.52646 1.26760 2.21510
2.18679 2.11109 2.22748 2.15799 2.19254 2.10149 1.95849
1.95410 2.09208 2.20012 2.35931 2.09430 1.76616
Celegans 1.76125 1.75264 1.79666 1.83984 1.56561 0.93929 0.92102
0.68977 0.00000 0.82927 0.83411 0.82261 1.08129 1.12595
1.16485 1.26465 1.31936 1.28450 1.46446 1.30824 2.32601
2.31638 2.12185 2.24472 2.14986 2.01173 1.94276 2.04733
2.07639 2.07349 2.23945 2.29314 2.10525 1.58431
Saccharomy 1.68309 1.66618 1.67357 1.71432 1.51343 0.84401 0.91222
0.76977 0.82927 0.00000 0.56633 0.90502 1.13499 1.17379
1.11372 1.25035 1.27180 1.35951 1.43430 1.33915 2.37325
2.31727 2.17583 2.28067 2.13491 2.12193 1.99895 1.98364
2.01087 2.19724 2.22189 2.41594 2.15533 1.93808
Schizosacc 1.72183 1.74112 1.66841 1.74593 1.57107 0.83309 0.86726
0.72571 0.83411 0.56633 0.00000 0.89001 1.04375 1.05966
1.14056 1.20298 1.23667 1.32791 1.47161 1.22250 2.37770
2.27862 2.12576 2.28871 2.07306 2.13595 2.06405 2.01469
1.99308 2.21232 2.44537 2.42905 2.17997 1.76501
Nosema 1.62609 1.58566 1.49526 1.54715 1.60786 0.93571 0.92873
0.82487 0.82261 0.90502 0.89001 0.00000 0.92147 0.83732
0.94991 1.09921 1.17881 1.12397 1.33265 1.43014 1.98390
2.05723 1.95464 1.97553 2.02089 2.06903 1.92177 1.86433
1.79532 1.89850 2.35001 2.04711 2.10972 1.80481
Chlamydia 1.62444 1.68293 1.56123 1.62377 1.68523 1.06893 1.18796
1.05110 1.08129 1.13499 1.04375 0.92147 0.00000 0.40638
1.01719 1.08902 1.19800 1.25840 1.35877 1.12875 2.21119
2.21386 2.16848 2.20311 2.10982 2.11571 2.06530 1.92061
1.93548 2.07445 2.00274 2.20402 2.08894 1.57355
Chlamydoph 1.59652 1.71314 1.57282 1.64810 1.59856 1.11156 1.22325
1.08427 1.12595 1.17379 1.05966 0.83732 0.40638 0.00000
1.02039 1.11614 1.21224 1.22226 1.35288 1.14239 2.22819
2.38336 2.17521 2.25801 2.20121 2.17474 2.16871 1.97977
2.04133 2.14405 2.11061 2.33951 2.08148 1.68138
Borrelia 1.49644 1.58563 1.50145 1.59895 1.47444 1.14439 1.14487
1.11446 1.16485 1.11372 1.14056 0.94991 1.01719 1.02039
0.00000 0.86878 1.21345 1.18716 1.23609 1.12214 2.15710
2.25742 2.10132 2.29480 2.17246 2.13688 2.08216 1.89219
1.94096 1.99749 2.14517 2.28749 2.13295 1.83657
Treponema 1.64214 1.78505 1.64148 1.75406 1.62763 1.21164 1.35315
1.21505 1.26465 1.25035 1.20298 1.09921 1.08902 1.11614
0.86878 0.00000 1.14386 1.30162 1.41298 1.17309 2.31773
2.37874 2.19740 2.20740 2.15954 2.31944 2.18690 1.98026
2.04754 2.25724 2.22747 2.30069 2.25695 1.75354
Mycobacter 1.54037 1.77980 1.61629 1.71761 1.60691 1.26524 1.35543
1.22727 1.31936 1.27180 1.23667 1.17881 1.19800 1.21224
1.21345 1.14386 0.00000 0.89501 1.35075 1.10609 2.23924
2.36547 2.08094 2.18881 2.09426 2.14840 1.98195 1.98426
2.07402 2.16453 2.19352 2.19946 2.26987 1.77801
Rickettsia 1.75741 1.74480 1.68327 1.80690 1.71063 1.30757 1.34877
1.29788 1.28450 1.35951 1.32791 1.12397 1.25840 1.22226
1.18716 1.30162 0.89501 0.00000 1.37422 1.33206 2.15867
2.24483 2.18167 2.26965 2.23462 2.24593 2.13557 2.10178
2.18641 2.13671 2.18584 2.25457 2.16359 1.87296
Staphyloco 1.43751 1.58626 1.51189 1.50418 1.36242 1.52960 1.50476
1.52646 1.46446 1.43430 1.47161 1.33265 1.35877 1.35288
1.23609 1.41298 1.35075 1.37422 0.00000 0.98226 1.99878
2.09400 2.01675 2.05216 2.22723 2.02781 1.90558 1.86135
1.85088 2.01435 1.92046 2.17029 2.07088 1.50272
Thermus 1.18206 1.31069 1.16658 1.30447 1.42564 1.27792 1.33845
1.26760 1.30824 1.33915 1.22250 1.43014 1.12875 1.14239
1.12214 1.17309 1.10609 1.33206 0.98226 0.00000 1.96708
2.04073 1.83837 2.00197 1.89435 1.86057 1.76258 1.61722
1.74615 1.75985 2.11191 1.78812 2.04568 1.50655
Helicobact 1.99893 1.96993 1.98418 1.95829 1.59044 2.28496 2.27132
2.21510 2.32601 2.37325 2.37770 1.98390 2.21119 2.22819
2.15710 2.31773 2.23924 2.15867 1.99878 1.96708 0.00000
0.84254 1.28342 1.33652 1.30426 1.36281 1.26103 1.24733
1.25865 1.21635 1.53349 1.31127 1.51203 2.21202
Campylobac 1.99646 1.95403 2.06993 1.93790 1.62586 2.27071 2.28403
2.18679 2.31638 2.31727 2.27862 2.05723 2.21386 2.38336
2.25742 2.37874 2.36547 2.24483 2.09400 2.04073 0.84254
0.00000 1.18643 1.29226 1.28351 1.32955 1.22109 1.20583
1.18158 1.15720 1.44552 1.30159 1.50535 2.31615
Haemophilu 1.85262 1.73718 1.75694 1.68421 1.32535 2.06482 2.16368
2.11109 2.12185 2.17583 2.12576 1.95464 2.16848 2.17521
2.10132 2.19740 2.08094 2.18167 2.01675 1.83837 1.28342
1.18643 0.00000 0.48887 0.73118 1.11634 1.02711 1.07703
1.02375 1.01401 1.29630 1.12055 1.53297 2.30101
Ecoli 2.06623 1.88188 1.96486 1.83541 1.48817 2.27591 2.23306
2.22748 2.24472 2.28067 2.28871 1.97553 2.20311 2.25801
2.29480 2.20740 2.18881 2.26965 2.05216 2.00197 1.33652
1.29226 0.48887 0.00000 0.76661 1.17285 1.08942 1.18079
1.13161 1.11962 1.33530 1.22295 1.61135 2.19543
Pseudomona 2.00965 1.92141 1.82155 1.82664 1.66060 2.11580 2.20921
2.15799 2.14986 2.13491 2.07306 2.02089 2.10982 2.20121
2.17246 2.15954 2.09426 2.23462 2.22723 1.89435 1.30426
1.28351 0.73118 0.76661 0.00000 1.26100 1.06569 1.14661
1.15513 1.13370 1.35295 1.20468 1.37735 2.33806
Streptococ 1.92417 1.87592 1.78722 1.79848 1.50741 2.09505 2.04114
2.19254 2.01173 2.12193 2.13595 2.06903 2.11571 2.17474
2.13688 2.31944 2.14840 2.24593 2.02781 1.86057 1.36281
1.32955 1.11634 1.17285 1.26100 0.00000 0.65197 1.09647
1.06806 1.19510 1.37350 1.17868 1.32549 2.32368
Bacillus 1.72876 1.73715 1.60983 1.62450 1.41627 1.99590 2.06201
2.10149 1.94276 1.99895 2.06405 1.92177 2.06530 2.16871
2.08216 2.18690 1.98195 2.13557 1.90558 1.76258 1.26103
1.22109 1.02711 1.08942 1.06569 0.65197 0.00000 0.96208
0.89733 1.07315 1.25844 0.97786 1.24336 2.25291
Fervidobac 1.61218 1.59416 1.57294 1.61501 1.34472 1.99116 2.04307
1.95849 2.04733 1.98364 2.01469 1.86433 1.92061 1.97977
1.89219 1.98026 1.98426 2.10178 1.86135 1.61722 1.24733
1.20583 1.07703 1.18079 1.14661 1.09647 0.96208 0.00000
0.45856 0.91580 1.24813 1.04619 1.36774 2.41642
Thermotoga 1.69248 1.64019 1.63334 1.60683 1.31330 2.03108 2.09193
1.95410 2.07639 2.01087 1.99308 1.79532 1.93548 2.04133
1.94096 2.04754 2.07402 2.18641 1.85088 1.74615 1.25865
1.18158 1.02375 1.13161 1.15513 1.06806 0.89733 0.45856
0.00000 0.90434 1.25595 1.05668 1.44946 2.55182
Aquifex 1.76808 1.73082 1.82259 1.71517 1.42109 2.03213 2.11774
2.09208 2.07349 2.19724 2.21232 1.89850 2.07445 2.14405
1.99749 2.25724 2.16453 2.13671 2.01435 1.75985 1.21635
1.15720 1.01401 1.11962 1.13370 1.19510 1.07315 0.91580
0.90434 0.00000 1.30177 1.12159 1.54673 2.54998
Ciona 1.99694 1.89911 1.99856 1.94878 1.76315 2.22733 2.17370
2.20012 2.23945 2.22189 2.44537 2.35001 2.00274 2.11061
2.14517 2.22747 2.19352 2.18584 1.92046 2.11191 1.53349
1.44552 1.29630 1.33530 1.35295 1.37350 1.25844 1.24813
1.25595 1.30177 0.00000 1.03461 1.46945 2.29367
Synechocys 2.05394 1.95529 1.95102 1.98014 1.53957 2.31224 2.37390
2.35931 2.29314 2.41594 2.42905 2.04711 2.20402 2.33951
2.28749 2.30069 2.19946 2.25457 2.17029 1.78812 1.31127
1.30159 1.12055 1.22295 1.20468 1.17868 0.97786 1.04619
1.05668 1.12159 1.03461 0.00000 1.50500 2.31641
Mycoplasma 1.91974 1.90691 1.74035 1.98560 1.81201 2.09318 2.16557
2.09430 2.10525 2.15533 2.17997 2.10972 2.08894 2.08148
2.13295 2.25695 2.26987 2.16359 2.07088 2.04568 1.51203
1.50535 1.53297 1.61135 1.37735 1.32549 1.24336 1.36774
1.44946 1.54673 1.46945 1.50500 0.00000 2.30693
Deinococcu 1.93543 1.87108 2.04272 1.93796 2.21132 1.62996 1.76102
1.76616 1.58431 1.93808 1.76501 1.80481 1.57355 1.68138
1.83657 1.75354 1.77801 1.87296 1.50272 1.50655 2.21202
2.31615 2.30101 2.19543 2.33806 2.32368 2.25291 2.41642
2.55182 2.54998 2.29367 2.31641 2.30693 0.00000
Average distance (over all possible pairs of sequences): 1.67207
TREE SEARCH
Quartet puzzling is used to choose from the possible tree topologies
and to simultaneously infer support values for internal branches.
Number of puzzling steps: 10000
Analysed quartets: 46376
Unresolved quartets: 1307 (= 2.8%)
Quartet trees are based on approximate maximum likelihood values
using the selected model of substitution and rate heterogeneity.
QUARTET PUZZLING TREE
Support for the internal branches of the unrooted quartet puzzling
tree topology is shown in percent.
This quartet puzzling tree is not completely resolved!
:---Fervidobac
:-----90:
: :---Thermotoga
:
: :---Streptococ
:-----87:
: :---Bacillus
:
: :---Haemophilu
: :-92:
:-81: :---Ecoli
: :
:-----------------99: :-------Pseudomona
: :
: : :---Helicobact
: :-----80:
: : :---Campylobac
: :
: : :---Ciona
: :-----68:
: : :---Synechocys
: :
: :-----------Aquifex
: :
: :-----------Mycoplasma
:
: :---Mycobacter
:-90: :-----------------96:
: : : :---Rickettsia
: : :
: : : :---Borrelia
: : : :-------------80:
: : :-98: : :---Treponema
: : : : :
: : : : : :---Chlamydia
: : : : :-------------77:
: : : : : :---Chlamydoph
: : : : :
: : : :-58: :---Arabidopsi
: : : : :-----95:
: : : : : :---Tetrahymen
: : : : :
: : : : :-74: :---Saccharomy
: :-98: : : : :-96:
:-92: : : : : : :---Schizosacc
: : : : : :-72:
: : : :-56: : :---Homosapien
: : : : :-79:
: : : : :---Celegans
: : : :
: : : :---------------Nosema
: : :
: : : :---Staphyloco
: : : :-67:
: : :-----------------82: :---Thermus
: : :
: : :-------Deinococcu
: :
: : :---METHANOBAC
: :-----------------------------68:
: : :---Archaeoglo
: :
: :-----------------------------------Sulfolobus
:
:---------------------------------------Methanococ
:
:---------------------------------------Pyrococcus
Quartet puzzling tree (in CLUSTAL W notation):
(Pyrococcus,((((Fervidobac,Thermotoga)90,(Streptococ,Bacillus)87,
((Haemophilu,Ecoli)92,Pseudomona)81,(Helicobact,Campylobac)80,
(Ciona,Synechocys)68,Aquifex,Mycoplasma)99,(((Mycobacter,
Rickettsia)96,((Borrelia,Treponema)80,(Chlamydia,Chlamydoph)77,
(((Arabidopsi,Tetrahymen)95,((Saccharomy,Schizosacc)96,(Homosapien,
Celegans)79)72)74,Nosema)56)58)98,((Staphyloco,Thermus)67,
Deinococcu)82)98)90,(METHANOBAC,Archaeoglo)68,Sulfolobus)92,
Methanococ);
BIPARTITIONS
The following bipartitions occured at least once in all intermediate
trees that have been generated in the 10000 puzzling steps:
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen)
********** ********** .......... ...* : 9920
*****..... .......... ********** ***. : 9821
*****..... ........** ********** **** : 9813
*********. .********* ********** **** : 9647
********** ******..** ********** **** : 9596
*****..*** ********** ********** **** : 9531
********** ********** **..****** **** : 9220
**........ .......... .......... .... : 9211
*****..... .......... .......... .... : 9043
********** ********** *******..* **** : 9004
********** ********** *****..*** **** : 8706
********** ********.. ********** ***. : 8207
********** ********** **...***** **** : 8084
********** ********** ..******** **** : 7984
********** ****..**** ********** **** : 7965
*******..* ********** ********** **** : 7894
********** **..****** ********** **** : 7696
*****..... .********* ********** **** : 7350
*******... .********* ********** **** : 7164
**..****** ********** ********** **** : 6841
********** ********** ********** ..** : 6827
********** ********.. ********** **** : 6698
*****..... ......**** ********** **** : 5793
*****..... ..******** ********** **** : 5569
Bipartitions not included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen)
****...... .......... .......... .... : 4700
********** ********** .......... ..** : 4677
********** ********** *******... **** : 4563
********** **....**** ********** **** : 4185
**...***** ********** ********** **** : 3592
********** ********** ..*******. **** : 3591
********** ********** ********** ...* : 3525
********** ********.* ********** ***. : 3257
***..***** ********** ********** **** : 3017
********** ********** *****..*** ..** : 2865
********** *...****** ********** **** : 2854
********** ****....** ********** **** : 2648
*****..... ....****** ********** **** : 2565
********** ********** .....****. **** : 2247
********** ********** .....***** **** : 2182
********** *.....**** ********** **** : 2125
********** ********** ********** .*.* : 2068
********** ********** .......... **** : 2002
********** ********** ..*****... **** : 1902
*******... ..******** ********** **** : 1868
(663 other less frequent bipartitions not shown)
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK)
Branch lengths are computed using the selected model of
substitution and rate heterogeneity.
:---28 Fervidobac
:----35
: :---29 Thermotoga
:
: :-----26 Streptococ
:----36
: :---27 Bacillus
:
: :---23 Haemophilu
: :--37
: : :----24 Ecoli
:----38
: :-----25 Pseudomona
:---------41
: : :-----21 Helicobact
: :------39
: : :-----22 Campylobac
: :
: : :--------31 Ciona
: :----40
: : :-----32 Synechocys
: :
: :-------30 Aquifex
: :
: :------------33 Mycoplasma
:---56
: : :-----17 Mycobacter
: : :---42
: : : :------18 Rickettsia
: : :---52
: : : : :----15 Borrelia
: : : : :---43
: : : : : :------16 Treponema
: : : :--51
: : : : :---13 Chlamydia
: : : :-----44
: : : : :---14 Chlamydoph
: : : :
: : : : :-----6 Arabidopsi
: : : : :--45
: : : : : :-----7 Tetrahymen
: : : : :--49
: : : : : : :----10 Saccharomy
: : : : : : :--46
: : : : : : : :---11 Schizosacc
: : : : : :-48
: : : : : : :----8 Homosapien
: : : : : :--47
: : : : : :-----9 Celegans
: : : :--50
: : : :------12 Nosema
: :----55
: : :-------19 Staphyloco
: : :-53
: : : :-----20 Thermus
: :--54
: :-------------34 Deinococcu
:--58
: : :----3 METHANOBAC
: :-57
: : :-----4 Archaeoglo
: :
: :--------5 Sulfolobus
:
:-----2 Methanococ
:
:----1 Pyrococcus
branch length S.E. branch length S.E.
Pyrococcus 1 0.36287 0.02714 35 0.31183 0.02714
Methanococ 2 0.46471 0.03081 36 0.33540 0.02898
METHANOBAC 3 0.36771 0.02742 37 0.14652 0.02104
Archaeoglo 4 0.46086 0.03043 38 0.36389 0.03053
Sulfolobus 5 0.67250 0.05097 39 0.50184 0.03835
Arabidopsi 6 0.45624 0.02997 40 0.32188 0.03716
Tetrahymen 7 0.44674 0.02905 41 0.82793 0.05325
Homosapien 8 0.31863 0.02430 42 0.27854 0.02877
Celegans 9 0.40611 0.02675 43 0.22330 0.02548
Saccharomy 10 0.29825 0.02290 44 0.38941 0.02933
Schizosacc 11 0.27819 0.02213 45 0.10885 0.02046
Nosema 12 0.51747 0.04059 46 0.17736 0.02011
Chlamydia 13 0.19777 0.01917 47 0.15216 0.02069
Chlamydoph 14 0.21281 0.01960 48 0.06677 0.01691
Borrelia 15 0.37055 0.02835 49 0.16276 0.02468
Treponema 16 0.51769 0.03296 50 0.18347 0.02537
Mycobacter 17 0.41513 0.03086 51 0.14756 0.02258
Rickettsia 18 0.48907 0.03297 52 0.19593 0.02660
Staphyloco 19 0.57923 0.03783 53 0.01375 0.02251
Thermus 20 0.43827 0.03493 54 0.11650 0.02494
Helicobact 21 0.45918 0.03447 55 0.31677 0.03394
Campylobac 22 0.39523 0.03248 56 0.21735 0.02991
Haemophilu 23 0.20495 0.02064 57 0.08135 0.01853
Ecoli 24 0.28985 0.02369 58 0.11165 0.01925
Pseudomona 25 0.41136 0.02985
Streptococ 26 0.40644 0.02919
Bacillus 27 0.24831 0.02354
Fervidobac 28 0.24632 0.02228
Thermotoga 29 0.22078 0.02131
Aquifex 30 0.58902 0.03597
Ciona 31 0.71078 0.06381
Synechocys 32 0.41704 0.03764
Mycoplasma 33 1.10237 0.05858 31 iterations until convergence
Deinococcu 34 1.16013 0.11829 log L: -60928.65
Quartet puzzling tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
(Pyrococcus:0.36287,((((Fervidobac:0.24632,Thermotoga:0.22078)90:0.31183,
(Streptococ:0.40644,Bacillus:0.24831)87:0.33540,((Haemophilu:0.20495,
Ecoli:0.28985)92:0.14652,Pseudomona:0.41136)81:0.36389,(Helicobact:0.45918,
Campylobac:0.39523)80:0.50184,(Ciona:0.71078,Synechocys:0.41704)
68:0.32188,Aquifex:0.58902,Mycoplasma:1.10237)99:0.82793,(((Mycobacter:0.41513,
Rickettsia:0.48907)96:0.27854,((Borrelia:0.37055,Treponema:0.51769)
80:0.22330,(Chlamydia:0.19777,Chlamydoph:0.21281)77:0.38941,(((Arabidopsi:0.45624,
Tetrahymen:0.44674)95:0.10885,((Saccharomy:0.29825,Schizosacc:0.27819)
96:0.17736,(Homosapien:0.31863,Celegans:0.40611)79:0.15216)72:0.06677)
74:0.16276,Nosema:0.51747)56:0.18347)58:0.14756)98:0.19593,((Staphyloco:0.57923,
Thermus:0.43827)67:0.01375,Deinococcu:1.16013)82:0.11650)98:0.31677)
90:0.21735,(METHANOBAC:0.36771,Archaeoglo:0.46086)68:0.08135,Sulfolobus:0.67250)
92:0.11165,Methanococ:0.46471);
TIME STAMP
Date and time: Fri Jun 18 17:52:49 1999
Runtime: 19991 seconds (= 333.2 minutes = 5.6 hours)