mpi56.bst

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

      Tested 83 alternative trees
      Ln Likelihood =  -14026.96738
      Doing local rearrangements
      Tested 82 alternative trees
   vaucheria-
      Tested 85 alternative trees
      Ln Likelihood =  -14246.98786
      Doing local rearrangements
      Tested 84 alternative trees
      Ln Likelihood =  -14246.95910
      Tested 84 alternative trees
   cryptomona
      Tested 87 alternative trees
      Ln Likelihood =  -14651.06409
      Doing local rearrangements
      Tested 86 alternative trees
      Ln Likelihood =  -14650.88545
      Tested 86 alternative trees
   costaria--
      Tested 89 alternative trees
      Ln Likelihood =  -14691.50056
      Doing local rearrangements
      Tested 88 alternative trees
   gloeothece
      Tested 91 alternative trees
      Ln Likelihood =  -14844.78701
      Doing local rearrangements
      Tested 90 alternative trees
      Ln Likelihood =  -14844.34180
      Tested 90 alternative trees
      Ln Likelihood =  -14844.20226
      Tested 90 alternative trees
   mycobactrm
      Tested 93 alternative trees
      Ln Likelihood =  -15097.85512
      Doing local rearrangements
      Tested 92 alternative trees
   pandorina-
      Tested 95 alternative trees
      Ln Likelihood =  -15165.25602
      Doing local rearrangements
      Tested 94 alternative trees
      Ln Likelihood =  -15164.55333
      Tested 94 alternative trees
   codium----
      Tested 97 alternative trees
      Ln Likelihood =  -15705.30419
      Doing local rearrangements
      Tested 96 alternative trees
      Ln Likelihood =  -15701.94654
      Tested 96 alternative trees
      Ln Likelihood =  -15701.81826
      Tested 96 alternative trees
   draparnald
      Tested 99 alternative trees
      Ln Likelihood =  -15892.83075
      Doing local rearrangements
      Tested 98 alternative trees
   nitella---
      Tested 101 alternative trees
      Ln Likelihood =  -16040.33604
      Doing local rearrangements
      Tested 100 alternative trees
   prochlthx-
      Tested 103 alternative trees
      Ln Likelihood =  -16231.11329
      Doing local rearrangements
      Tested 102 alternative trees
      Ln Likelihood =  -16229.58167
      Tested 102 alternative trees
   flexistips
      Tested 105 alternative trees
      Ln Likelihood =  -16640.54739
      Doing local rearrangements
      Tested 104 alternative trees
   mantoniell
      Tested 107 alternative trees
      Ln Likelihood =  -16818.16838
      Doing local rearrangements
      Tested 106 alternative trees
      Ln Likelihood =  -16817.52671
      Tested 106 alternative trees
      Ln Likelihood =  -16808.56518
      Tested 106 alternative trees
      Ln Likelihood =  -16808.56508
      Tested 106 alternative trees

Examined 9438 trees

                  +------ deinonema-
               +-49  
               !  !    +- Taquaticus
               !  +---50  
               !       +- Tthermophi
               !  
               !                   +---- mycobactrm
               !              +---53  
               !           +-52    +------- micrococcu
               !           !  !  
               !        +-51  +------- streptococ
               !        !  !  
               !        !  !  +-------------- myco-gentl
               !     +--4  +-54  
               !     !  !     +------- bacteroide
               !     !  !  
               !     !  !  +------- pseudomona
               !     !  +--1  
               !  +--5     !  +---- shewanella
               !  !  !     +--2  
               !  !  !        !  + ecoli-----
               !  !  !        +--3  
        +-----45  !  !           + salmonella
        !      !  !  !  
        !      !  !  +------ bacillus--
        !      !  !  
        !      !  !          +------ mantoniell
        !      !  !          !  
        !      !  !          !              +--------- cryptomona
        !      !  !          !           +-13  
        !      !  !          !           !  +------- vaucheria-
        !      !  !          !           !  
        !      !  !          !        +-12  +------- gracilaria
        !      !  !          !        !  !  !  
        !      !  !          !        !  !  !     +- smithora--
        !      !  !          !        !  +-14  +-16  
        !      !  !          !        !     !  !  +---- porphyra--
        !      !  !          !        !     !  !  
        !      !  !          !        !     +-15     +------ cyanophora
        !      !  !          !        !        !  +-18  
        !      !  !          !        !        !  !  +------------ ochromonas
        !      !  !          !        !        +-17  
        !      !  !          !        !           !  +------ porphyridi
        !      !  !          !     +-11           !  !  
        !      +--6          !     !  !           +-19         + costaria--
        !         !          !     !  !              !  +-----21  
        !         !       +--8     !  !              !  !      + laminaria-
        !         !       !  !     !  !              +-20  
        !         !       !  !     !  !                 !  +- cyclotella
        !         !       !  !     !  !                 +-22  
        !         !       !  !     !  !                    !  +- coscinodis
        !         !       !  !     !  !                    +-23  
        !         !       !  !     !  !                       +-- odontella-
        !         !       !  !     !  !  
        !         !       !  !  +-10  !  +- raphidonem
        !         !       !  !  !  !  +-24  
        !         !       !  !  !  !     !      +- euglena---
        !         !       !  !  !  !     +-----25  
        !         !       !  !  !  !            +------- astasia---
        !         !       !  !  !  !  
        !         !       !  !  !  !     +- chlorella-
        !         !       !  !  !  !  +-27  
        !         !       !  !  !  !  !  !  +------- draparnald
   +---46         !       !  !  !  !  !  +-28  
   !    !         !       !  !  !  !  !     !  +- pandorina-
   !    !         !       !  !  !  !  !     +-29  
   !    !         !       !  !  !  +-26        !  + chlamydomo
   !    !         !       !  +--9     !        +-30  
   !    !         !       !     !     !           + gonium----
   !    !         !       !     !     !  
   !    !         !       !     !     !         +---------- codium----
   !    !         +-------7     !     !      +-32  
   !    !                 !     !     +-----31  +--------- derbesia--
   !    !                 !     !            !  
   !    !                 !     !            +---- bryopsis--
   !    !                 !     !  
   !    !                 !     !       +------------------------------ coleochaet
   !    !                 !     !  +---34  
   !    !                 !     !  !    !  +---- nitella---
   !    !                 !     !  !    +-35  
   !    !                 !     +-33       +-- chara-----
   !    !                 !        !  
   !    !                 !        !            +- glycine---
   !    !                 !        +-----------36  
   !    !                 !                     !  +---- arabidopsi
--48    !                 !                     +-37  
   !    !                 !                        !  + nico-syl-A
   !    !                 !                        +-38  
   !    !                 !                           + nico-tabac
   !    !                 !  
   !    !                 !        +---- gloeothece
   !    !                 !     +-41  
   !    !                 !     !  +---- anacystis-
   !    !                 !  +-40  
   !    !                 !  !  !  +------- spirulina-
   !    !                 !  !  +-42  
   !    !                 !  !     !  +--------- gloeobacte
   !    !                 +-39     +-43  
   !    !                    !        +------- plectonema
   !    !                    !  
   !    !                    !  +------- prochlthx-
   !    !                    +-44  
   !    !                       +------ phormidium
   !    !  
   !    !  +------- flexistips
   !    +-47  
   !       +-------------------- ChlamydiaB
   !  
   +------------------- borrelia-b
   !  
   +--------- thermotoga

Remember: this is an unrooted tree!

Ln Likelihood =  -16808.56586

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
  48            46              0.04980     (  0.02872,     0.07164) **
  46            45              0.06173     (  0.04026,     0.08400) **
  45            49              0.04190     (  0.02548,     0.05878) **
  49          deinonema-        0.06578     (  0.04605,     0.08618) **
  49            50              0.05334     (  0.03518,     0.07207) **
  50          Taquaticus        0.01678     (  0.00737,     0.02633) **
  50          Tthermophi        0.01604     (  0.00684,     0.02538) **
  45             6              0.01188     (     zero,     0.02459) **
   6             5              0.02334     (  0.00955,     0.03746) **
   5             4              0.03312     (  0.01768,     0.04897) **
   4            51              0.01677     (  0.00341,     0.03044) **
  51            52              0.02970     (  0.01387,     0.04596) **
  52            53              0.06280     (  0.04206,     0.08429) **
  53          mycobactrm        0.03914     (  0.02320,     0.05551) **
  53          micrococcu        0.08517     (  0.06252,     0.10870) **
  52          streptococ        0.09306     (  0.06869,     0.11846) **
  51            54              0.03289     (  0.01654,     0.04970) **
  54          myco-gentl        0.14631     (  0.11593,     0.17831) **
  54          bacteroide        0.09254     (  0.06841,     0.11769) **
   4             1              0.02487     (  0.01098,     0.03909) **
   1          pseudomona        0.07341     (  0.05228,     0.09531) **
   1             2              0.02799     (  0.01431,     0.04199) **
   2          shewanella        0.04256     (  0.02702,     0.05850) **
   2             3              0.03580     (  0.02141,     0.05053) **
   3          ecoli-----        0.00000     (     zero,     0.00656)
   3          salmonella        0.00430     (     zero,     0.01029) **
   5          bacillus--        0.07471     (  0.05366,     0.09653) **
   6             7              0.08101     (  0.05830,     0.10462) **
   7             8              0.01159     (  0.00230,     0.02103) **
   8          mantoniell        0.07106     (  0.04603,     0.09717) **
   8             9              0.00000     (     zero,     0.00649)
   9            10              0.01575     (  0.00501,     0.02668) **
  10            11              0.02147     (  0.00929,     0.03390) **
  11            12              0.02060     (  0.00844,     0.03302) **
  12            13              0.01358     (  0.00174,     0.02566) **
  13          cryptomona        0.09924     (  0.07468,     0.12484) **
  13          vaucheria-        0.07823     (  0.05124,     0.10650) **
  12            14              0.01867     (  0.00606,     0.03155) **
  14          gracilaria        0.08470     (  0.05726,     0.11346) **
  14            15              0.01121     (  0.00112,     0.02147) **
  15            16              0.03391     (  0.01765,     0.05062) **
  16          smithora--        0.00843     (     zero,     0.01757) **
  16          porphyra--        0.03847     (  0.02187,     0.05553) **
  15            17              0.01677     (  0.00329,     0.03056) **
  17            18              0.02117     (  0.00571,     0.03705) **
  18          cyanophora        0.06123     (  0.03781,     0.08561) **
  18          ochromonas        0.11897     (  0.08549,     0.15444) **
  17            19              0.02833     (  0.01208,     0.04503) **
  19          porphyridi        0.06411     (  0.03966,     0.08960) **
  19            20              0.03204     (  0.01454,     0.05008) **
  20            21              0.06309     (  0.03870,     0.08851) **
  21          costaria--        0.00686     (     zero,     0.01483) **
  21          laminaria-        0.01180     (  0.00180,     0.02197) **
  20            22              0.03168     (  0.01455,     0.04931) **
  22          cyclotella        0.02529     (  0.00994,     0.04104) **
  22            23              0.01291     (  0.00089,     0.02517) **
  23          coscinodis        0.02776     (  0.01196,     0.04398) **
  23          odontella-        0.04106     (  0.02194,     0.06081) **
  11            24              0.00910     (     zero,     0.01998) **
  24          raphidonem        0.02133     (  0.00687,     0.03614) **
  24            25              0.07531     (  0.05357,     0.09786) **
  25          euglena---        0.01349     (     zero,     0.02837) **
  25          astasia---        0.07224     (  0.04654,     0.09909) **
  10            26              0.02682     (  0.01163,     0.04241) **
  26            27              0.02179     (  0.00587,     0.03814) **
  27          chlorella-        0.02608     (  0.00990,     0.04270) **
  27            28              0.02165     (  0.00689,     0.03678) **
  28          draparnald        0.08944     (  0.06095,     0.11936) **
  28            29              0.01471     (  0.00114,     0.02859) **
  29          pandorina-        0.01346     (  0.00273,     0.02439) **
  29            30              0.02821     (  0.01309,     0.04372) **
  30          chlamydomo        0.00000     (     zero,     0.00593)
  30          gonium----        0.01035     (  0.00132,     0.01952) **
  26            31              0.06860     (  0.04084,     0.09772) **
  31            32              0.04135     (  0.01689,     0.06685) **
  32          codium----        0.12122     (  0.08871,     0.15559) **
  32          derbesia--        0.09505     (  0.06413,     0.12765) **
  31          bryopsis--        0.05087     (  0.02791,     0.07474) **
   9            33              0.04144     (  0.02296,     0.06051) **
  33            34              0.03958     (  0.02079,     0.05898) **
  34          coleochaet        0.31572     (  0.26712,     0.36862) **
  34            35              0.04334     (  0.02308,     0.06432) **
  35          nitella---        0.04710     (  0.02543,     0.06959) **
  35          chara-----        0.02504     (  0.00840,     0.04215) **
  33            36              0.11809     (  0.09024,     0.14730) **
  36          glycine---        0.02247     (  0.01029,     0.03490) **
  36            37              0.01841     (  0.00731,     0.02972) **
  37          arabidopsi        0.05638     (  0.03893,     0.07435) **
  37            38              0.04318     (  0.02782,     0.05894) **
  38          nico-syl-A        0.00000     (     zero,     0.00248)
  38          nico-tabac        0.00000     (     zero,     0.00243)
   7            39              0.01179     (  0.00192,     0.02182) **
  39            40              0.00886     (  0.00067,     0.01717) **
  40            41              0.02372     (  0.00875,     0.03907) **
  41          gloeothece        0.04791     (  0.02734,     0.06921) **
  41          anacystis-        0.05374     (  0.03200,     0.07630) **
  40            42              0.00944     (  0.00013,     0.01890) **
  42          spirulina-        0.08792     (  0.06492,     0.11184) **
  42            43              0.01878     (  0.00208,     0.03596) **
  43          gloeobacte        0.10267     (  0.07113,     0.13597) **
  43          plectonema        0.08651     (  0.05793,     0.11652) **
  39            44              0.01774     (  0.00355,     0.03228) **
  44          prochlthx-        0.07743     (  0.05115,     0.10490) **
  44          phormidium        0.06620     (  0.04157,     0.09189) **
  46            47              0.02093     (  0.00570,     0.03655) **
  47          flexistips        0.08426     (  0.06016,     0.10937) **
  47          ChlamydiaB        0.21057     (  0.17243,     0.25130) **
  48          borrelia-b        0.20035     (  0.16247,     0.24079) **
  48          thermotoga        0.10599     (  0.07842,     0.13490) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Tree also written to /N/hpcscr/dkberry/fastDNAml_1.2.2p/testdata/mpi56.trf