
P A U P *
Portable version 4.0b10 for Unix
Thu Aug 31 10:55:16 2006

      -----------------------------NOTICE-----------------------------
        This is a beta-test version.  Please report any crashes,
        apparent calculation errors, or other anomalous results.
        There are no restrictions on publication of results obtained
        with this version, but you should check the WWW site
        frequently for bug announcements and/or updated versions.  
        See the README file on the distribution media for details.
      ----------------------------------------------------------------

MaxTrees reset to 1000

Processing of file
"... /MethodsExpressPhylogeneticsExamples/A_parsimony_paup/data.nex" begins...

Data read in DNA format

Data matrix has 12 taxa, 250 characters
Valid character-state symbols: ACGT
Missing data identified by '?'
Gaps identified by '-'
"Equate" macros in effect:
   R,r ==> {AG}
   Y,y ==> {CT}
   M,m ==> {AC}
   K,k ==> {GT}
   S,s ==> {CG}
   W,w ==> {AT}
   H,h ==> {ACT}
   B,b ==> {CGT}
   V,v ==> {ACG}
   D,d ==> {AGT}
   N,n ==> {ACGT}

Processing of file
"... /MethodsExpressPhylogeneticsExamples/A_parsimony_paup/data.nex" completed.

Bootstrap method with heuristic search:
  Number of bootstrap replicates = 1000
  Starting seed = 418648093
  Optimality criterion = parsimony
    Character-status summary:
      Of 250 total characters:
        All characters are of type 'unord'
        All characters have equal weight
        52 characters are constant
        29 variable characters are parsimony-uninformative
        Number of parsimony-informative characters = 169
    Gaps are treated as "missing"
  Starting tree(s) obtained via stepwise addition
  Addition sequence: simple (reference taxon = taxon 1)
  Number of trees held at each step during stepwise addition = 1
  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
  Steepest descent option not in effect
  Initial 'MaxTrees' setting = 1000 (will be auto-increased by 100)
  Branches collapsed (creating polytomies) if maximum branch length is zero
  'MulTrees' option in effect
  Topological constraints not enforced
  Trees are unrooted

   1000 bootstrap replicates completed
   Time used = 3 sec (CPU time = 3.22 sec)

Bootstrap 50% majority-rule consensus tree

/------------------------------------------------------------------------------ taxon 1(1)
|
|                                                       /---------------------- taxon 2(2)
|                                                       |
|                                            /----96----+          /----------- taxon 9(9)
|                                            |          \----69----+
|                                            |                     \----------- taxon 12(12)
|                                /----98-----+
|                                |           |                     /----------- taxon 6(6)
|                                |           \---------74----------+
|                     /----68----+                                 \----------- taxon 11(11)
|                     |          |
|                     |          |                                 /----------- taxon 4(4)
|          /----87----+          \---------------77----------------+
|          |          |                                            \----------- taxon 7(7)
|          |          |
+----83----+          \-------------------------------------------------------- taxon 8(8)
|          |
|          |                                                       /----------- taxon 5(5)
|          \--------------------------81---------------------------+
|                                                                  \----------- taxon 10(10)
|
\------------------------------------------------------------------------------ taxon 3(3)

Bipartitions found in one or more trees and frequency of occurrence (bootstrap support
values):

         1 1
123456789012      Freq      %
-----------------------------
.*...*..*.**    980.05  98.0%
.*......*..*    962.58  96.3%
.*.*.****.**    867.80  86.8%
.*.*********    830.72  83.1%
....*....*..    814.43  81.4%
...*..*.....    765.18  76.5%
.....*....*.    741.10  74.1%
........*..*    690.47  69.0%
.*.*.**.*.**    682.22  68.2%
.*......*...    309.53  31.0%
.*...*.**.**    216.37  21.6%
.*......*.**    178.17  17.8%
.*...**.*.**    128.13  12.8%
.*.******.**     94.93   9.5%
.*...*..*..*     77.07   7.7%
.***.****.**     63.70   6.4%
.*...****.**     59.00   5.9%
.*.*.*******     54.63   5.5%

67 groups at (relative) frequency less than 5% not shown

1 tree saved to file
"... /MethodsExpressPhylogeneticsExamples/A_parsimony_paup/bootTree.nex"
