/usr/share/doc/fastdnaml/examples/test5I.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)
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 = -336.11996
Sequence5
Tested 5 alternative trees
Ln Likelihood = -365.80850
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 = -365.80850
Between And Length Approx. Confidence Limits
------- --- ------ ------- ---------- ------
2 3 0.08775 ( 0.02504, 0.15802) **
3 Sequence5 0.01873 ( zero, 0.05038) *
3 Sequence4 0.06742 ( 0.01738, 0.12217) **
2 1 0.06940 ( 0.01393, 0.13070) **
1 Sequence2 0.05346 ( 0.00521, 0.10607) **
1 Sequence3 0.06177 ( 0.01061, 0.11786) **
2 Sequence1 0.08289 ( 0.02281, 0.14988) **
* = significantly positive, P < 0.05
** = significantly positive, P < 0.01
Tree also written to treefile.24370
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