cout << "deconvolute(fasta=yourFastaFile) " << "\n";
}else if (globaldata->helpRequest == "dist.seqs") {
cout << "The dist.seqs command reads a file containing sequences and creates a distance file." << "\n";
- cout << "The dist.seqs command parameters are fasta, phylip, clustal, nexus, calc, ends, cutoff and processors. " << "\n";
+ cout << "The dist.seqs command parameters are fasta, phylip, clustal, nexus, calc, countends, cutoff and processors. " << "\n";
cout << "You must use one of the following parameters for your filename: fasta, phylip, clustal or nexus. " << "\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 ends 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 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, but you can use up to 4 processors." << "\n";
cout << "The dist.seqs command should be in the following format: " << "\n";
- cout << "dist.seqs(fasta=yourFastaFile, calc=yourCalc, ends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) " << "\n";
- cout << "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, ends=F, cutoff= 2.0, processors=3)." << "\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";
}else if (globaldata->helpRequest == "align.seqs") {
cout << "The align.seqs command reads a file containing sequences and creates an alignment file and a report file." << "\n";
- cout << "The align.seqs command parameters are fasta, phylip, clustal, nexus, template, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
- cout << "You must use one of the following parameters for your candidate filename: fasta, phylip, clustal or nexus. " << "\n";
+ cout << "The align.seqs command parameters are fasta, candidate, search, ksize, align, match, mismatch, gapopen and gapextend. " << "\n";
cout << "The template parameter is also required." << "\n";
- cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is suffix." << "\n";
- cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is blast." << "\n";
+ cout << "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer." << "\n";
+ cout << "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman." << "\n";
cout << "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7." << "\n";
cout << "The match parameter allows you to specify the bonus for having the same base. The default is 1.0." << "\n";
cout << "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0." << "\n";
- cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0." << "\n";
+ cout << "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0." << "\n";
cout << "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0." << "\n";
cout << "The align.seqs command should be in the following format: " << "\n";
- cout << "align.seqs(fasta=yourFastaFile, template=yourTemplateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
- cout << "Example align.seqs(fasta=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
+ cout << "align.seqs(fasta=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) " << "\n";
+ cout << "Example align.seqs(candidate=candidate.fasta, fasta=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)" << "\n";
cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "collect.single") {
cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "get.group") {
- cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
+ cout << "The get.group command can only be executed after a successful read.otu command." << "\n";
+//cout << "The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the concensus command." << "\n";
cout << "You may not use any parameters with the get.group command." << "\n";
cout << "The get.group command should be in the following format: " << "\n";
cout << "get.group()" << "\n";
cout << "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels)." << "\n";
cout << "Example dist.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund)." << "\n";
cout << "The default value for groups is all the groups in your groupfile." << "\n";
- cout << "There is no default value for calc." << "\n";
+ cout << "The default value for calc is jclass and thetayc." << "\n";
validCalcs->printCalc("matrix", cout);
- cout << "The dist.shared command outputs a .matrix file for each calculator you specify at each distance you choose." << "\n";
+ cout << "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose." << "\n";
cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
}else if (globaldata->helpRequest == "bootstrap.shared") {
cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
projects / mothur.git / blobdiff