testalign-methods {pairseqsim} | R Documentation |
Computes optimal pairwise alignment of 2 protein sequences. For internal use.
obj1 |
see above |
obj2 |
see above |
sub |
Substitution matrix |
delta |
gap opening penalty |
gapext |
gap extension penalty |
alignment |
type of alignment: c("global","local","overlap") |
scoring |
type of scoring, identity, similarity, score, scoreN, pozitive |
For two objects of class AASequence
returns an object of class
AAAlignment
.\
Otherwise it returns a score. If used with NULL as second parameter it
returns a distance matrix. The scores are transformed into
distances. For details see the vignette.
Witold E. Wolski