#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
#include "reversecommand.h"
#include "trimseqscommand.h"
#include "mergefilecommand.h"
commands["screen.seqs"] = "screen.seqs";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
commands["screen.seqs"] = "screen.seqs";
commands["reverse.seqs"] = "reverse.seqs";
commands["trim.seqs"] = "trim.seqs";
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
else if(commandName == "tree.shared") { command = new TreeGroupCommand(optionString); }
else if(commandName == "dist.shared") { command = new MatrixOutputCommand(optionString); }
else if(commandName == "bootstrap.shared") { command = new BootSharedCommand(optionString); }
else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
else if(commandName == "dist.seqs") { command = new DistanceCommand(optionString); }
else if(commandName == "align.seqs") { command = new AlignCommand(optionString); }
else if(commandName == "summary.seqs") { command = new SeqSummaryCommand(optionString); }
else if(commandName == "screen.seqs") { command = new ScreenSeqsCommand(optionString); }
else if(commandName == "reverse.seqs") { command = new ReverseSeqsCommand(optionString); }
else if(commandName == "trim.seqs") { command = new TrimSeqsCommand(optionString); }
else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
else { command = new NoCommand(optionString); }
else if(commandName == "merge.files") { command = new MergeFileCommand(optionString); }
else { command = new NoCommand(optionString); }