
P A U P *
Portable version 4.0b10 for Unix
Fri Feb 15 15:56:18 2008

      -----------------------------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.
      ----------------------------------------------------------------

Optimality criterion set to likelihood.

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   0.514700   1.395800   0.943600
           0.514700          -   1.481000   3.345500
           1.395800   1.481000          -   1.000000
           0.943600   3.345500   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.22870  C=0.26210  G=0.34260  T=0.16660
      Among-site rate variation:
        Assumed proportion of invariable sites  = none
        Distribution of rates at variable sites = gamma (discrete approximation)
          Shape parameter (alpha)   = 0.3731
          Number of rate categories = 4
          Representation of average rate for each category = mean
      These settings correspond to the GTR+G model
      Number of distinct data patterns under this model = 217
      Molecular clock not enforced
      Starting branch lengths obtained using Rogers-Swofford approximation method
      Trees with approximate likelihoods 5% or further from the target score are rejected without additional iteration
      Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06
      -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities
  Starting tree(s) obtained via stepwise addition
  Addition sequence: as-is
  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 = 100
  Branches collapsed (creating polytomies) if branch length is less than or equal to 1e-08
  'MulTrees' option in effect
  Topological constraints not enforced
  Trees are unrooted

Heuristic search completed
   Total number of rearrangements tried = 12
   Score of best tree(s) found = 4479.56778
   Number of trees retained = 1
   Time used = <1 sec (CPU time = 0.18 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 6
    Substitution rate-matrix parameters estimated via ML
    Nucleotide frequencies estimated via ML
    Among-site rate variation:
      Assumed proportion of invariable sites  = none
      Distribution of rates at variable sites = gamma (discrete approximation)
        Shape parameter (alpha)   = estimated
        Number of rate categories = 4
        Representation of average rate for each category = mean
    These settings correspond to the GTR+G model
    Number of distinct data patterns under this model = 217
    Molecular clock not enforced
    Starting branch lengths obtained using Rogers-Swofford approximation method
    Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, delta=1e-06
    -ln L (unconstrained) = unavailable due to missing-data and/or ambiguities

Tree             1
------------------
-ln L   4479.56772
Base frequencies:
  A       0.228702
  C       0.262137
  G       0.342645
  T       0.166516
Rate matrix R:
  AC       0.51467
  AG       1.39576
  AT       0.94359
  CG       1.48099
  CT       3.34549
  GT       1.00000
Shape     0.373146

Time used to compute likelihoods = 2 sec (CPU time = 1.63 sec)

1 tree saved to file "~/Write/Teach/N_winter_2008/G_practicals/PeterPracticals/6_heuristic_search/bestTree.nex"
