/usr/share/doc/phylip/examples/tests/dnaml.ok is in phylip 1:3.696+dfsg-5.
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 | Nucleic acid sequence Maximum Likelihood method, version 3.6b
Settings for this run:
U Search for best tree? Yes
T Transition/transversion ratio: 2.0000
F Use empirical base frequencies? Yes
C One category of sites? Yes
R Rate variation among sites? constant rate
W Sites weighted? No
S Speedier but rougher analysis? Yes
G Global rearrangements? No
J Randomize input order of sequences? No. Use input order
O Outgroup root? No, use as outgroup species 1
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? (none)
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Write out trees onto tree file? Yes
5 Reconstruct hypothetical sequences? No
Y to accept these or type the letter for one to change
[2J[HNucleic acid sequence Maximum Likelihood method, version 3.6b
Settings for this run:
U Search for best tree? Yes
T Transition/transversion ratio: 2.0000
F Use empirical base frequencies? Yes
C One category of sites? Yes
R Rate variation among sites? constant rate
W Sites weighted? No
S Speedier but rougher analysis? Yes
G Global rearrangements? No
J Randomize input order of sequences? No. Use input order
O Outgroup root? No, use as outgroup species 1
M Analyze multiple data sets? No
I Input sequences interleaved? Yes
0 Terminal type (IBM PC, ANSI, none)? IBM PC
1 Print out the data at start of run No
2 Print indications of progress of run Yes
3 Print out tree Yes
4 Write out trees onto tree file? Yes
5 Reconstruct hypothetical sequences? No
Y to accept these or type the letter for one to change
Adding species:
1. Bovine
2. Mouse
3. Gibbon
4. Orang
5. Gorilla
6. Chimp
7. Human
Output written to file "outfile"
Tree also written onto file "outtree"
Done.
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