| Calling Sequence | CircularTour(seqs)
CircularTour(AllAll) CircularTour(Dist) | |||||||||||||||
| Parameters |
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| Return Type | list(posint) | |||||||||||||||
| Synopsis | This is a front-end to ComputeTSP where we give as input either a set of sequences or a distance matrix or an AllAll matrix and the result is a minimal cost tour broken at the most convenient place (highest cost). The input can be: | |||||||||||||||
List of sequences - n sequences. The sequences are aligned all against all using Global alignments with the default DM matrix. (the rest is as with AllAll matrix). | ||||||||||||||||
AllAll matrix - an n x n symmetric matrix of Alignments. If the Alignments have a PamDistance, the minimal cost tour is based on PamDistances. If not it is based on maximizing the Score of the neighbouring alignments. | ||||||||||||||||
Distance matrix - an n x n symmetric distance matrix. The tour is computed to minimize the sum of the distances. | ||||||||||||||||
The output is the list of indices in the best tour of length n. | ||||||||||||||||
| Examples | > seqs := [SSSS, AAAA, AAAS, AASS, ASSS, SSSA, SSAA, SAAA]: > CircularTour(seqs); [5, 4, 3, 2, 8, 7, 6, 1] | |||||||||||||||
| See also | Clusters, ComputeTSP, FindCircularOrder, MAlign | |||||||||||||||