The file PHYLIP_NOTES:DISTANCE.DOC summarises four distance-based methods for nucleic and protein sequences. Fitch-Margoliash using "the PHYLIP search method" and Neighbour-Joining do not assume rate constancy across lineages. The UPGMA and KITSCH programs assume rate constancy across lineages. The FITCH and Neighbour-joining methods are equally preferred, with NJ the faster program.
$ Neighbor
PHYLIP version 3.5c - running NEIGHBOR
Input file name (* NEIGHBOR.DAT *) ? : rna.dist
Output file name
(* RNA.OUT *) ? : neighbor.out
Treefile name to WRITE (*
NEIGHBOR.TREE *) ? :
Submit as batch job (* No *) ? :
Neighbor-Joining/UPGMA method version 3.5
Settings for this run:
N Neighbor-joining or UPGMA tree? Neighbor-joining
O
Outgroup root? No, use as outgroup species 1
L
Lower-triangular data matrix? No
R Upper-triangular data matrix?
No
S Subreplicates? No
J Randomize input
order of species? No. Use input order
M Analyze multiple data
sets? No
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
3 Print out tree Yes
4 Write out
trees onto tree file? Yes
Are these settings correct? (type Y or the letter for one to change)
The output file NEIGHBOR.OUT gives a phylogenetic tree.
Use the same distance data for FITCH:
$ fitch
PHYLIP version 3.5c - running FITCH
Input file name (* FITCH.DAT *) ? : rna.dist
Output file name (*
RNA.OUT *) ? : fitch.out
Treefile name to WRITE (* FITCH.TREE *) ? :
Submit as batch job (* No *) ? :
Accept the defaults and examine the output file FITCH.OUT.
Do the trees produced by the two programs differ, or are they the same?
The programs DRAWGRAM and DRAWTREE can be used to display the TREE files.
RETREE can be used to rearrange the nodes on the trees.