DNADIST calculates pairwise distances between sequences, taking into account (for DNA) transitions and transversions. NB: There are four different methods for doing this in DNADIST!
$ dnadist
PHYLIP version 3.5c - running DNADIST
Input file name (* DNADIST.DAT *) ? : rna.phy
Output file name (*
RNA.OUT *) ? : rna.dist
Submit as batch job (* No *) ? :
Nucleic
acid sequence Distance Matrix program, version 3.53c
Settings for this run:
D Distance (Kimura, Jin/Nei, ML, J-C)? Kimura
2-parameter
T Transition/transversion ratio? 2.0
C One
category of substitution rates? Yes
L Form of distance
matrix? Square
M Analyze multiple data sets? No
I
Input sequences interleaved? Yes
0 Terminal type (IBM PC, VT52, ANSI)?
ANSI
1 Print out the data at start of run No
2 Print indications
of progress of run Yes
Are these settings correct? (type Y or letter for one to
change)
y
Examine the distances file RNA.DIST