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"
16 Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
17 A Fast Distance-Based Phylogenetic Tree Construction Method,
18 J. Mol. Evol., 62, 785-792
21 /****************************************************************************/
23 class ClearcutCommand : public Command {
26 ClearcutCommand(string);
30 vector<string> setParameters();
31 string getCommandName() { return "clearcut"; }
32 string getCommandCategory() { return "Hypothesis Testing"; }
34 string getHelpString();
35 string getOutputPattern(string);
36 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"; }
37 string getDescription() { return "create a tree from a fasta or phylip file"; }
40 void help() { m->mothurOut(getHelpString()); }
43 string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
44 bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA;
46 vector<string> outputNames;
50 /****************************************************************************/