forester/test_data/paup_log_test_1

   1 P A U P *
   2 Version 4.0b10 for 32-bit Microsoft Windows
   3 Fri Mar 21 18:53:11 2008
   4
   5       -----------------------------NOTICE-----------------------------
   6         This is a beta-test version.  Please report any crashes,
   7         apparent calculation errors, or other anomalous results.
   8         There are no restrictions on publication of results obtained
   9         with this version, but you should check the WWW site
  10         frequently for bug announcements and/or updated versions.
  11         See the README file on the distribution media for details.
  12       ----------------------------------------------------------------
  13
  14 Tree description:
  15
  16   Unrooted tree(s) rooted using outgroup method
  17   Optimality criterion = parsimony
  18     Character-status summary:
  19       Of 4978 total characters:
  20         All characters are of type 'unord'
  21         All characters have equal weight
  22         419 characters are constant
  23         3179 variable characters are parsimony-uninformative
  24         Number of parsimony-informative characters = 1380
  25     Character-state optimization: Accelerated transformation (ACCTRAN)
  26
  27 Tree number 1 (rooted using default outgroup)
  28
  29 Data matrix and reconstructed states for internal nodes:
  30
  31                      111111111122222222223333333333444444444455555555556666666
  32 Taxon/Node  123456789012345678901234567890123456789012345678901234567890123456
  33 ------------------------------------------------------------------------------
  34 MOUSE       000001111101100010110110001010111111110001111001001110101110001111
  35 NEMVE       000001111000000000010100001000000000100001011110110001110101110111
  36 MONBE       000001100001000100010001011111100000000001011000000000000000000100
  37 DICDI       111101100000011001010100001000000000001110011000000000000000000000
  38 ARATH       000011100010000001011000101010100000001000011000000000000000000000
  39 6           000001100000000001010000001010100000001000011000000000000000000000
  40 7           000001100000000000010000001010100000000001011000000000000000000100
  41 8           000001111000000000010100001010100000100001011000000000100100000111
  42
  43 Data matrix and reconstructed states for internal nodes (continued):
  44
  45
  46             444444444444444444444444444444444444444444444444444444444444444444
  47             888888888888888999999999999999999999999999999999999999999999999999
  48             888889999999999000000000011111111112222222222333333333344444444445
  49 Taxon/Node  567890123456789012345678901234567890123456789012345678901234567890
  50 ------------------------------------------------------------------------------
  51 MOUSE       111110110111001001011110100001111101011101011011100111101011111100
  52 NEMVE       111100100110000001011110101110011100100001111000010001101011011100
  53 MONBE       011110100100000111011110000000011000000000010100000000101110001000
  54 DICDI       000101101100010001100010010000011100010011010000000000101010000000
  55 ARATH       010101101100100011111111001110011110000000010000001000110010000011
  56 6           010101101100000011111110000000011100000000010000000000101010000000
  57 7           011100100100000011011110000000011100000000010000000000101010001000
  58 8           111100100110000001011110100000011100000001011000000001101011011100
  59
  60 Data matrix and reconstructed states for internal nodes (continued):
  61
  62             4444444444444444444444444444
  63             9999999999999999999999999999
  64             5555555556666666666777777777
  65 Taxon/Node  1234567890123456789012345678
  66 ----------------------------------------
  67 MOUSE       1100111010111111101011011110
  68 NEMVE       0100001000101101101000010010
  69 MONBE       1100001100001111000000001010
  70 DICDI       0110011000101100110001100001
  71 ARATH       0111111001001100110110001010
  72 6           0110011000001100110000001010
  73 7           0100001000001101100000001010
  74 8           0100001000101101101000011010
  75
  76 Tree length = 5111
  77 Consistency index (CI) = 0.8920
  78 Homoplasy index (HI) = 0.1080
  79 CI excluding uninformative characters = 0.7143
  80 HI excluding uninformative characters = 0.2857
  81 Retention index (RI) = 0.6000
  82 Rescaled consistency index (RC) = 0.5352
  83
  84 /------------------------------------------------------------ MOUSE
  85 |
  86 +--------------- NEMVE
  87 8
  88 |                              /---------------------------- MONBE
  89 |                              |
  90 \------------------------------7         /---------------------- DICDI
  91                                \---------6
  92                                          \------------------------------ ARATH
  93
  94 /----------------------------------------------------------------------- MOUSE
  95 |
  96 +----------------------------------------------------------------------- NEMVE
  97 8
  98 |                       /----------------------------------------------- MONBE
  99 |                       |
 100 \-----------------------7                      /------------------------ DICDI
 101                         \----------------------6
 102                                                \------------------------ ARATH
 103
 104 Character change lists:
 105
 106 Character                                CI  Steps           Changes
 107 ------------------------------------------------------------------------------
 108 1 (14-3-3=BRCT)                       1.000      1    node_6 0 ==> 1 DICDI
 109 2 (14-3-3=PARP)                       1.000      1    node_6 0 ==> 1 DICDI
 110 3 (14-3-3=VIT)                        1.000      1    node_6 0 ==> 1 DICDI
 111 4 (14-3-3=VWA)                        1.000      1    node_6 0 ==> 1 DICDI
 112 5 (2-Hacid_dh_C=ACT)                  1.000      1    node_6 0 ==> 1 ARATH
 113 8 (2OG-FeII_Oxy=Methyltransf_11)      1.000      1    node_8 1 ==> 0 node_7
 114 9 (2OG-FeII_Oxy=P4Ha_N)               1.000      1    node_8 1 ==> 0 node_7
 115 10 (2OG-FeII_Oxy=RRM_1)               1.000      1    node_8 0 ==> 1 MOUSE
 116 11 (2OG-FeII_Oxy=ShK)                 1.000      1    node_6 0 ==> 1 ARATH
 117 12 (2OG-FeII_Oxy=TPR_2)               0.500      1    node_8 0 --> 1 MOUSE
 118                                                  1    node_7 0 --> 1 MONBE
 119