/usr/share/doc/fastdnaml/examples/test5TF.out is in fastdnaml 1.2.2-12.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | 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
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 41 distinct data patterns (columns)
Base Frequencies:
A 0.25000
C 0.25000
G 0.25000
T(U) 0.25000
Transition/transversion ratio = 0.501000
(Transition/transversion parameter = 0.001000)
Adding species:
Sequence1
Sequence2
Sequence3
Sequence4
Tested 3 alternative trees
Ln Likelihood = -342.76283
Sequence5
Tested 5 alternative trees
Ln Likelihood = -371.36406
Doing local rearrangements
Tested 4 alternative trees
Examined 13 trees
+------ Sequence5
+----------------------------------3
! +--------------------------- Sequence4
---2
! +--------------------------- Sequence2
+---------------------------1
! +--------------------------- Sequence3
!
+---------------------------------- Sequence1
Remember: this is an unrooted tree!
Ln Likelihood = -371.36406
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
2 3 0.07952 ( 0.02075, 0.14329) **
3 Sequence5 0.02019 ( zero, 0.05147) *
3 Sequence4 0.06439 ( 0.01576, 0.11638) **
2 1 0.06948 ( 0.01584, 0.12726) **
1 Sequence2 0.05617 ( 0.00822, 0.10739) **
1 Sequence3 0.05714 ( 0.00917, 0.10839) **
2 Sequence1 0.08148 ( 0.02287, 0.14505) **
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
Tree also written to treefile.24382
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