P A U P *
Portable version 4.0b10 for Unix
Fri Jun  2 00:50:34 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.
      ----------------------------------------------------------------

Processing of file "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2429.fasta"
begins...

Warning: Use of all-digit taxon and/or character names does not conform to the
         NEXUS standard and is strongly discouraged.  Remember that names have
         priority over numbers.

Data read in DNA format

Data matrix has 7 taxa, 249 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 "~/new_at_family_tcoffee/4_20/cds_nex_4_20/2429.fasta"
completed.

Optimality criterion set to likelihood.

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 2 (HKY85 variant)
      Transition/transversion ratio = 0.9675 (kappa = 1.9738011)
      Assumed nucleotide frequencies (set by user):
        A=0.32530  C=0.18200  G=0.22180  T=0.27090
      Among-site rate variation:
        Assumed proportion of invariable sites  = none
        Distribution of rates at variable sites = equal
      These settings correspond to the HKY85 model
      Number of distinct data patterns under this model = 99
      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) = 1021.04760
  Starting tree(s) obtained via stepwise addition
  Addition sequence: random
    Number of replicates = 10
    Starting seed = 1323435796
  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

Note: Approximation limit dynamically readjusted to 11.039981

Heuristic search completed
   Total number of rearrangements tried = 144
   Score of best tree(s) found = 1159.91927
   Number of trees retained = 2
   Time used = <1 sec (CPU time = 0.65 sec)

Tree-island profile:
                     First      Last                     First   Times
Island      Size      tree      tree        Score    replicate     hit
----------------------------------------------------------------------
     1         2         1         2   1159.91927            1      10

Tree description:

  Unrooted tree(s) rooted using outgroup method
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 2 (HKY85 variant)
      Transition/transversion ratio = 0.9675 (kappa = 1.9738011)
      Assumed nucleotide frequencies (set by user):
        A=0.32530  C=0.18200  G=0.22180  T=0.27090
      Among-site rate variation:
        Assumed proportion of invariable sites  = none
        Distribution of rates at variable sites = equal
      These settings correspond to the HKY85 model
      Number of distinct data patterns under this model = 99
      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) = 1021.04760

Tree number 1 (rooted using default outgroup)

Branch lengths and linkages for tree #1 (unrooted)

                    Connected          Branch    Standard
   Node              to node           length       error
---------------------------------------------------------
110565 (1)              11            0.30470     0.04202
    10                  11            1.36761     0.19141
39028 (2)               10                  0     0.01583
     9                  10            0.02777     0.01232
     8                   9            0.02624     0.01208
6917 (3)                 8            0.00828     0.00591
77118 (4)                8            0.00386     0.00412
At4g39880.1 (5)          9            0.29604     0.04144
AtCg00840 (6)           11                  0   undefined
AtCg01300 (7)           11                  0   undefined
---------------------------------------------------------
Sum                                   2.03451

-Ln likelihood = 1159.91927

/------------ 110565
|
|                                                    / 39028
|                                                    |
|                                                    | /- 6917
+---------------------------------------------------10/8
11                                                   ||\- 77118
|                                                    \9
|                                                     \------------ At4g39880.1
|
+ AtCg00840
|
\ AtCg01300

2 trees saved to file "~/new_at_family_tcoffee/4_20/trees_4_20/2429.ml.tre"