- cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
- cout << "The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. " << "\n";
- cout << "The fasta parameter is required." << "\n";
- cout << "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap." << "\n";
- cout << "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T." << "\n";
- cout << "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0." << "\n";
- cout << "The processors parameter allows you to specify number of processors to use. The default is 1." << "\n";
- cout << "The dist.seqs command should be in the following format: " << "\n";
- cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
- cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3)." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc)." << "\n" << "\n";
+ mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
+ mothurOut("The dist.seqs command parameters are fasta, calc, countends, cutoff and processors. \n");
+ mothurOut("The fasta parameter is required.\n");
+ mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
+ mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n");
+ mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
+ mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
+ mothurOut("The dist.seqs command should be in the following format: \n");
+ mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
+ mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");