
fastDNAml, version 1.2.1, March 9, 1998

Based on Joseph Felsenstein's

   Nucleic acid sequence Maximum Likelihood method, version 3.3

5 Species, 114 Sites

Quick add (only local branches initially optimized) in effect

Site category   Rate of change

           1        0.062
           2        0.125
           3        0.250
           4        0.500
           5        1.000
           6        2.000
           7        4.000
           8        8.000
           9       16.000
           A       32.000

Rearrangements of partial trees may cross 1 branch.
Rearrangements of full tree may cross 1 branch.

Total weight of positions in analysis = 60
There are 42 distinct data patterns (columns)

Empirical Base Frequencies:

   A       0.21812
   C       0.25686
   G       0.30872
  T(U)     0.21630

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.531841)

Adding species:
   Sequence1
   Sequence2
   Sequence3
   Sequence4
      Tested 3 alternative trees
      Ln Likelihood =    -192.11599
   Sequence5
      Tested 5 alternative trees
      Ln Likelihood =    -207.45621
      Doing local rearrangements
      Tested 4 alternative trees
      Ln Likelihood =    -206.60058
      Tested 4 alternative trees

Examined 17 trees

                                            + Sequence5
   +----------------------------------------3  
   !                                        +---------------- Sequence4
---1  
   !                +------------------------ Sequence2
   +----------------2  
   !                +---------------------------------------- Sequence3
   !  
   +-------------------------------- Sequence1

Remember: this is an unrooted tree!

Ln Likelihood =    -206.60058

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   1             3              0.07563     (     zero,     0.16305) **
   3          Sequence5         0.01329     (     zero,     0.04273)
   3          Sequence4         0.04488     (     zero,     0.10050) **
   1             2              0.02816     (     zero,     0.08381)
   2          Sequence2         0.05576     (     zero,     0.12600) **
   2          Sequence3         0.08145     (  0.00425,     0.17027) **
   1          Sequence1         0.06884     (     zero,     0.14680) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01


Tree also written to treefile.24391

