| Calling Sequence
| MAlignment(InputSeqs,AlignedSeqs,labels,method,PrintOrder,Score,UpperBound,tree,AllAll)
|
| Parameters
| | Name | Type | Description |
|
| InputSeqs
| list(string) | input sequences (before alignment) |
| AlignedSeqs
| list(string) | aligned sequences (in input order) |
| labels
| list(string) | labels for the sequences (in input order) |
| method
| string | method(s) that generated the MSA |
| PrintOrder
| list(integer) | order used for printing and scoring |
| Score
| numeric | score of the MSA (circular tour) |
| UpperBound
| numeric | upper bound score (circular tour) |
| tree
| Tree | tree used by the probabilistic method |
| AllAll
| matrix | all against all Alignment matrix |
|
| Methods
| PartialOrderMSA, print, Rand, select, string |
| Synopsis
| An MAlignment stores the information of a multiple
sequence alignment.
The sequences may contain proteins or DNA.
The Score and UpperBound (on the score) are calculated using the
circular tour method.
In order to force recalculation of the score, use the selector RecalcScore.
A MAlignment is normally created by calling MAlign. |
| See also
| Align, Alignment, MAlign |