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