1 #ifndef CLEARCUTCOMMAND_H
2 #define CLEARCUTCOMMAND_H
8 * Created by westcott on 5/11/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "globaldata.hpp"
17 Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
18 A Fast Distance-Based Phylogenetic Tree Construction Method,
19 J. Mol. Evol., 62, 785-792
22 /****************************************************************************/
24 class ClearcutCommand : public Command {
27 ClearcutCommand(string);
28 ~ClearcutCommand() {};
33 string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
34 bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
38 /****************************************************************************/