/usr/share/doc/phylip/examples/tests/dnapars.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 63 64 65 66 67 | DNA parsimony algorithm, version 3.6b
Setting for this run:
U Search for best tree? Yes
S Search option? More thorough search
V Number of trees to save? 10000
J Randomize input order of sequences? No. Use input order
O Outgroup root? No, use as outgroup species 1
T Use Threshold parsimony? No, use ordinary parsimony
N Use Transversion parsimony? No, count all steps
W Sites weighted? No
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 Print out steps in each site No
5 Print sequences at all nodes of tree No
6 Write out trees onto tree file? Yes
Y to accept these or type the letter for one to change
[2J[H
DNA parsimony algorithm, version 3.6b
Setting for this run:
U Search for best tree? Yes
S Search option? More thorough search
V Number of trees to save? 10000
J Randomize input order of sequences? No. Use input order
O Outgroup root? No, use as outgroup species 1
T Use Threshold parsimony? No, use ordinary parsimony
N Use Transversion parsimony? No, count all steps
W Sites weighted? No
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 Print out steps in each site No
5 Print sequences at all nodes of tree No
6 Write out trees onto tree file? Yes
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
Doing global rearrangements on all trees tied for best
!-------------!
.............
.............
Collapsing best trees
.
Output written to file "outfile"
Tree also written onto file "outtree"
Done.
|