An example of a PHYLIP menu (from the program DNAML) |
Nucleic acid sequence Maximum Likelihood method, version 3.68
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)? ANSI
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