Line | |
---|
1 | #Please insert up references in the next lines (line starts with keyword UP) |
---|
2 | UP arb.hlp |
---|
3 | UP glossary.hlp |
---|
4 | UP pars.hlp |
---|
5 | UP mode_kernlin.hlp |
---|
6 | UP mode_optimize.hlp |
---|
7 | |
---|
8 | #Please insert subtopic references (line starts with keyword SUB) |
---|
9 | #SUB subtopic.hlp |
---|
10 | |
---|
11 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
---|
12 | |
---|
13 | #************* Title of helpfile !! and start of real helpfile ******** |
---|
14 | TITLE NNI (Nearest Neighbour Interchange) |
---|
15 | |
---|
16 | DESCRIPTION Searches for a better (more parsimonious) tree by swapping the |
---|
17 | relative positions of subtrees separated by one edge. |
---|
18 | At each inner edge (i.e. at non-leaf edges) three different |
---|
19 | topologies are possible. |
---|
20 | |
---|
21 | Testing these 3 possible topologies and keeping the best of them, |
---|
22 | is called "Nearest Neighborhood Interchange" (NNI). |
---|
23 | |
---|
24 | SECTION Possible topologies tested by NNI |
---|
25 | |
---|
26 | The 3 different topologies checked by performing a NNI are |
---|
27 | |
---|
28 | (A,B,C = subtrees; R = rest of tree) |
---|
29 | |
---|
30 | R R R |
---|
31 | \ \ \ |
---|
32 | /\ /\ /\ |
---|
33 | A \ B \ C \ |
---|
34 | /\ /\ /\ |
---|
35 | B C A C B A |
---|
36 | |
---|
37 | |
---|
38 | Note: there are no other possible topologies containing A,B,C and R! |
---|
39 | |
---|
40 | WARNINGS None |
---|
41 | |
---|
42 | BUGS No bugs known |
---|
Note: See
TracBrowser
for help on using the repository browser.