testalign-methods: Scoring of optimal alingments.
In wolski/pairseqsim: pairwise sequence alignment similarity simple.

Description Arguments Value Methods Author(s) References

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.