test5c.bst

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

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 = 114
There are 73 distinct data patterns (columns)

Empirical Base Frequencies:

   A       0.18570
   C       0.24823
   G       0.31783
  T(U)     0.24823

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.571835)

Adding species:
   Sequence1
   Sequence2
   Sequence3
   Sequence4
      Tested 3 alternative trees
      Ln Likelihood =    -381.89787
   Sequence5
      Tested 5 alternative trees
      Ln Likelihood =    -418.08178
      Doing local rearrangements
      Tested 4 alternative trees
      Ln Likelihood =    -412.77783
      Tested 4 alternative trees

Examined 17 trees

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

Remember: this is an unrooted tree!

Ln Likelihood =    -412.77783

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   1             3              0.01052     (  0.00196,     0.01921) **
   3          Sequence5         0.00190     (     zero,     0.00530) **
   3          Sequence4         0.00816     (  0.00172,     0.01468) **
   1             2              0.00773     (  0.00062,     0.01493) **
   2          Sequence3         0.00748     (  0.00094,     0.01410) **
   2          Sequence2         0.00620     (  0.00021,     0.01225) **
   1          Sequence1         0.01103     (  0.00235,     0.01983) **

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


Tree also written to treefile.24364