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- createAlignment (Sequence seq1, Sequence seq2, ...) — returns the alignment created from the sequences.
- addToAlignment (MAlignment aln, Sequence seq, int row = -1) — adds the sequence to the specified row of the alignment. If the “row” parameter is not specified the sequence is added to the end of the alignment.
- sequenceFromAlignment (MAlignment aln, int row) — returns the sequence from the specified row of the alignment.
- findInAlignment (MAlignment aln, Sequence seq) — searches the alignment for the specified string. Return the number of the row if the sequence has been found or “-1” if it hasn’t been found.
- findInAlignment (MAlignment aln, QString name) — searches the alignment for a sequence with the specified name.
- removeFromAlignment (MAlignment aln, int row) — removes a sequence from the specified row of the alignment.
- rowNum (MAlignment aln) — returns the number of rows in the alignment.
- columnNum (MAlignment aln) — returns the length of the alignment.
- alignmentAlphabetType (MAlignment aln) — returns the alignment’s alphabet.
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