
P A U P *
Portable version 4.0b10 for Unix
Fri Feb 15 15:59:46 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.
      ----------------------------------------------------------------

Processing of file "~/Write/Teach/N_winter_2008/G_practicals/PeterPracticals/9_sh_test/data.nex" begins...

Data read in DNA format

Data matrix has 12 taxa, 50 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 "~/Write/Teach/N_winter_2008/G_practicals/PeterPracticals/9_sh_test/data.nex" completed.

Neighbor-joining search settings:
  Ties (if encountered) will be broken systematically
  Distance measure = uncorrected ("p")
  (Tree is unrooted)

   Tree found by neighbor-joining method stored in tree buffer
   Time used = <1 sec (CPU time = 0.00 sec)

Neighbor-joining tree:

/------------------------------------------------------------------------------- A1
|
|          /------------------------------------------------------------------------ A2
|          |
|          |            /----------------------------------------------------------------------- A5
|          |    /-------+
+----------+    |       \--------------------------------------------------------- B4
|          |    |
|          |    |                      /------------------------------------------------------------------------------------------ A7
|          \----+             /--------+
|               |             |        \------------------------------------------------------------------------------------- A8
|               |      /------+
|               |      |      \----------------------------------------------------------------- B3
|               \------+
|                      |             /------------------------------------------------------- B1
|                      \-------------+
|                                    \-------------------------------------------------------------- B2
|
|                     /----------------------------------------------------------------- A3
|      /--------------+
|      |              \---------------------------------------------------- A6
\------+
       \------------------------------------------------------------ A4

Optimality criterion set to likelihood.

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.064500   1.982400   0.219800
           2.064500          -   0.747200   1.982400
           1.982400   0.747200          -   1.000000
           0.219800   1.982400   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0949
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: nearest-neighbor interchange (NNI)
  Initial swapping on tree 1 already in memory
  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 = 30
   Score of best tree(s) found = 638.70398
   Number of trees retained = 1
   Time used = <1 sec (CPU time = 0.35 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    638.57172
Rate matrix R:
  AC       2.08427
  AG       1.99063
  AT       0.11833
  CG       0.64071
  CT       1.99063
  GT       1.00000
P_inv    0.0952542

Time used to compute likelihoods = <1 sec (CPU time = 0.50 sec)

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.084265   1.990634   0.118325
           2.084265          -   0.640710   1.990634
           1.990634   0.640710          -   1.000000
           0.118325   1.990634   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0952542
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: subtree-pruning-regrafting (SPR)
  Initial swapping on tree 1 already in memory
  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 = 462
   Score of best tree(s) found = 638.02670
   Number of trees retained = 1
   Time used = 3 sec (CPU time = 2.60 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    637.96713
Rate matrix R:
  AC       2.19372
  AG       2.09651
  AT       0.12723
  CG       0.58148
  CT       2.09651
  GT       1.00000
P_inv    0.0957288

Time used to compute likelihoods = 1 sec (CPU time = 0.46 sec)

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.193725   2.096515   0.127225
           2.193725          -   0.581480   2.096515
           2.096515   0.581480          -   1.000000
           0.127225   2.096515   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0957288
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
  Initial swapping on tree 1 already in memory
  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 = 534
   Score of best tree(s) found = 637.96713
   Number of trees retained = 1
   Time used = 2 sec (CPU time = 2.79 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    637.96713
Rate matrix R:
  AC       2.19372
  AG       2.09651
  AT       0.12723
  CG       0.58148
  CT       2.09651
  GT       1.00000
P_inv    0.0957288

Time used to compute likelihoods = 1 sec (CPU time = 0.46 sec)

1 tree saved to file "~/Write/Teach/N_winter_2008/G_practicals/PeterPracticals/9_sh_test/ml_tree.nex"
   Forcing NJ tree to be compatible with constraint-tree "monoA"

Neighbor-joining search settings:
  Ties (if encountered) will be broken systematically
  Distance measure = uncorrected ("p")
  (Tree is unrooted)

   Note: Ties were encountered; neighbor-joining tree may not be unique

   Tree found by neighbor-joining method stored in tree buffer
   Time used = <1 sec (CPU time = 0.00 sec)

Neighbor-joining tree:

/------------------------------------------------------------------------------ A1
|
|         /------------------------------------------------------------------------ A2
|         |
|         |      /-------------------------------------------------------------------------- A5
+---------+      |
|         |      |                      /----------------------------------------------------------------------------------------- A7
|         |      |        /-------------+
|         \------+        |             \------------------------------------------------------------------------------------ A8
|                |        |
|                |        |                             /------------------------------------------------------ B1
|                \--------+         /-------------------+
|                         |         |                   \------------------------------------------------------------- B2
|                         |       /-+
|                         |       | \------------------------------------------------------------------ B4
|                         \.......+
|                                 \--------------------------------------------------------------------- B3
|
|                     /---------------------------------------------------------------- A3
|      /--------------+
|      |              \--------------------------------------------------- A6
\------+
       \----------------------------------------------------------- A4

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.064500   1.982400   0.219800
           2.064500          -   0.747200   1.982400
           1.982400   0.747200          -   1.000000
           0.219800   1.982400   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0949
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: nearest-neighbor interchange (NNI)
  Initial swapping on tree 1 already in memory
  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
  Keeping only trees compatible with constraint-tree "monoA"
  Trees are unrooted

Heuristic search completed
   Total number of rearrangements tried = 41
   Score of best tree(s) found = 639.35835
   Number of trees retained = 1
   Time used = 1 sec (CPU time = 0.52 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    639.02560
Rate matrix R:
  AC       2.29237
  AG       2.03309
  AT      0.077187
  CG       0.62806
  CT       2.03309
  GT       1.00000
P_inv    0.0956649

Time used to compute likelihoods = 1 sec (CPU time = 0.93 sec)

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.292370   2.033086  0.0771870
           2.292370          -   0.628059   2.033086
           2.033086   0.628059          -   1.000000
          0.0771870   2.033086   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0956649
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: subtree-pruning-regrafting (SPR)
  Initial swapping on tree 1 already in memory
  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
  Keeping only trees compatible with constraint-tree "monoA"
  Trees are unrooted

Heuristic search completed
   Total number of rearrangements tried = 144
   Score of best tree(s) found = 639.02560
   Number of trees retained = 1
   Time used = 1 sec (CPU time = 0.89 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    639.02560
Rate matrix R:
  AC       2.29237
  AG       2.03309
  AT      0.077187
  CG       0.62806
  CT       2.03309
  GT       1.00000
P_inv    0.0956649

Time used to compute likelihoods = 1 sec (CPU time = 0.93 sec)

Heuristic search settings:
  Optimality criterion = likelihood
    Likelihood settings:
      Number of substitution types  = 6
      User-specified substitution rate matrix =
                  -   2.292370   2.033086  0.0771870
           2.292370          -   0.628059   2.033086
           2.033086   0.628059          -   1.000000
          0.0771870   2.033086   1.000000          -
      Assumed nucleotide frequencies (set by user):
        A=0.25000  C=0.25000  G=0.25000  T=0.25000
      Among-site rate variation:
        Assumed proportion of invariable sites  = 0.0956649
        Distribution of rates at variable sites = equal
      These settings correspond to the GTR+I model
      Number of distinct data patterns under this model = 48
      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) = 192.82856
  Branch-swapping algorithm: tree-bisection-reconnection (TBR)
  Initial swapping on tree 1 already in memory
  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
  Keeping only trees compatible with constraint-tree "monoA"
  Trees are unrooted

Heuristic search completed
   Total number of rearrangements tried = 256
   Score of best tree(s) found = 639.02560
   Number of trees retained = 1
   Time used = 1 sec (CPU time = 1.47 sec)

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1
------------------
-ln L    639.02560
Rate matrix R:
  AC       2.29237
  AG       2.03309
  AT      0.077187
  CG       0.62806
  CT       2.03309
  GT       1.00000
P_inv    0.0956649

Time used to compute likelihoods = 1 sec (CPU time = 0.93 sec)

1 tree saved to file "~/Write/Teach/N_winter_2008/G_practicals/PeterPracticals/9_sh_test/constrained_tree.nex"

Processing TREES block from file "ml_tree.nex":
   Keeping: trees from file (replacing trees in memory)
   1 tree read from file
   Time used = <1 sec (CPU time = 0.00 sec)
   1 tree now in memory

Processing TREES block from file "constrained_tree.nex":
   Keeping: trees in memory plus trees from file
   1 tree originally in memory
   1 tree read from file
   1 tree from file kept
   Time used = <1 sec (CPU time = 0.00 sec)
   2 trees now in memory

Likelihood scores of tree(s) in memory:
  Likelihood settings:
    Number of substitution types  = 5 (restriction of 6ST GTR model)
    Substitution classification:   A C G T
                                 A - a b c
                                 C a - d b
                                 G b d - e
                                 T c b e -
    Assumed nucleotide frequencies (set by user):
      A=0.25000  C=0.25000  G=0.25000  T=0.25000
    Among-site rate variation:
      Assumed proportion of invariable sites  = estimated
      Distribution of rates at variable sites = equal
    These settings correspond to a submodel of the GTR+I model
    Number of distinct data patterns under this model = 48
    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) = 192.82856

Tree             1           2
------------------------------
-ln L    637.96713   639.02560
Rate matrix R:
  AC       2.19372     2.29237
  AG       2.09651     2.03309
  AT       0.12723    0.077187
  CG       0.58148     0.62806
  CT       2.09651     2.03309
  GT       1.00000     1.00000
P_inv    0.0957288   0.0956649

Time used to compute likelihoods = 2 sec (CPU time = 1.37 sec)

Shimodaira-Hasegawa test:
  SH test using RELL bootstrap (one-tailed test)
  Number of bootstrap replicates = 1000

    Tree         -ln L    Diff -ln L       P 
---------------------------------------------
       1     637.96713        (best)
       2     639.02560       1.05847   0.374 
