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#ifndef CLEARCUTCOMMAND_H
#define CLEARCUTCOMMAND_H
/*
* clearcutcommand.h
* Mothur
*
* Created by westcott on 5/11/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
/*
Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
A Fast Distance-Based Phylogenetic Tree Construction Method,
J. Mol. Evol., 62, 785-792
*/
/****************************************************************************/
class ClearcutCommand : public Command {
public:
ClearcutCommand(string);
~ClearcutCommand() = default;
vector<string> setParameters();
string getCommandName() { return "clearcut"; }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Sheneman L, Evans J, Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-4. \nhttp://www.mothur.org/wiki/Clearcut"; }
string getDescription() { return "create a tree from a fasta or phylip file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
bool abort;
vector<string> outputNames;
};
/****************************************************************************/
#endif
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