8 * Created by Pat Schloss on 12/17/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * This is my implementation of the NAST (nearest alignment space termination) algorithm as described in:
13 * DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, & Anderson GL. 2006. NAST: a multiple
14 * sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research. 34:W394-9.
16 * To construct an object one needs to provide a method of getting a pairwise alignment (alignment) and the template
17 * and candidate sequence that are to be aligned to each other.
22 #include "mothurout.h"
27 /**************************************************************************************************/
32 Nast(Alignment*, Sequence*, Sequence*);
34 float getSimilarityScore();
35 int getMaxInsertLength();
38 void pairwiseAlignSeqs();
39 void regapSequences();
40 void removeExtraGaps(string&, string, string);
43 Sequence* candidateSeq;
44 Sequence* templateSeq;
50 /**************************************************************************************************/