test5u.bst

来自「fastDNAml is an attempt to solve the sam」· BST 代码 · 共 156 行

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

User-supplied tree topology will be used.

Total weight of positions in analysis = 114
There are 41 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)

User-defined trees:


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

Remember: this is an unrooted tree!

Ln Likelihood =    -365.80850

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   1             2              0.06940     (  0.01393,     0.13070) **
   2          Sequence2         0.05346     (  0.00521,     0.10607) **
   2          Sequence3         0.06177     (  0.01061,     0.11786) **
   1             3              0.08775     (  0.02504,     0.15802) **
   3          Sequence4         0.06742     (  0.01738,     0.12217) **
   3          Sequence5         0.01873     (     zero,     0.05038) *
   1          Sequence1         0.08289     (  0.02281,     0.14988) **

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -374.57884

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   2          Sequence3         0.06867     (  0.01299,     0.13022) **
   2             1              0.00000     (     zero,     0.02880)
   1             3              0.14082     (  0.06276,     0.23097) **
   3          Sequence4         0.06155     (  0.01197,     0.11574) **
   3          Sequence5         0.02596     (     zero,     0.06481) **
   1          Sequence2         0.06268     (  0.00894,     0.12187) **
   2          Sequence1         0.14157     (  0.06516,     0.22951) **

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -372.26531

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   2          Sequence2         0.05076     (  0.00335,     0.10237) **
   2             1              0.02085     (     zero,     0.05426) *
   1             3              0.13281     (  0.05866,     0.21777) **
   3          Sequence4         0.05946     (  0.01021,     0.11325) **
   3          Sequence5         0.02831     (     zero,     0.06896) **
   1          Sequence3         0.05492     (  0.00578,     0.10858) **
   2          Sequence1         0.13541     (  0.06223,     0.21911) **

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



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

Remember: this is an unrooted tree!

Ln Likelihood =    -399.62271

 Between        And             Length      Approx. Confidence Limits
 -------        ---             ------      ------- ---------- ------
   1             2              0.01197     (     zero,     0.04296)
   2          Sequence2         0.11578     (  0.04568,     0.19547) **
   2          Sequence4         0.12038     (  0.04919,     0.20149) **
   1             3              0.00000     (     zero,     0.02449)
   3          Sequence3         0.10862     (  0.04249,     0.18322) **
   3          Sequence5         0.09735     (  0.03466,     0.16759) **
   1          Sequence1         0.10726     (  0.04319,     0.17925) **

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


Tree also written to treefile.24385

Tree      Ln L        Diff Ln L       Its S.D.   Significantly worse?

  1    -365.80850  <------ best
  2    -372.26531      -6.45680        6.6552            No
  3    -374.57884      -8.77033        5.3864            No
  4    -399.62271     -33.81420       11.7723           Yes