string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
+ string getDescription() { return "align sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+ string getDescription() { return "calculate AMOVA statistic"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+ string getDescription() { return "anosim"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Bin.seqs"; }
-
+ string getDescription() { return "maps sequences to otus"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
+ string getDescription() { return "bootstrap.shared"; }
int execute();
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
-
+ string getDescription() { return "estimate number of species"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Huber T, Faulkner G, Hugenholtz P (2004). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-9. \nhttp://www.mothur.org/wiki/Chimera.bellerophon"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+ string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
-
+ string getDescription() { return "trim sequence length"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
-
+ string getDescription() { return "find the concensus taxonomy for each OTU"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
-
+ string getDescription() { return "classify sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
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()); }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; }
+ string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6. \nhttp://www.mothur.org/wiki/Cluster.classic"; }
+ string getDescription() { return "cluster your sequences into OTUs using dotur's method"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
+ string getDescription() { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster.split"; }
+ string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.single"; }
string getHelpString();
+ string getDescription() { return "generates collector's curves using calculators, that describe the richness, diversity, and other features of individual samples"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "Schloss PD, Handelsman J (2006). Introducing SONS, A tool that compares the membership of microbial communities. Appl Environ Microbiol 72: 6773-9. \nhttp://www.mothur.org/wiki/Collect.shared"; }
-
+ string getDescription() { return "generates collector's curves for calculators, which describe the similarity between communities or their shared richness"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
virtual string getCommandCategory() = 0;
virtual string getHelpString() = 0;
virtual string getCitation() = 0;
+ virtual string getDescription() = 0;
virtual map<string, vector<string> > getOutputFiles() { return outputTypes; }
virtual vector<string> setParameters() = 0; //to fill parameters
~ConcensusCommand() {}
vector<string> setParameters();
- string getCommandName() { return "concensus"; }
+ string getCommandName() { return "consensus"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
-
+ string getDescription() { return "consensus"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+ string getDescription() { return "create a consensus sequence for each OTU or for a fasta file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
+ string getDescription() { return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
-
+ string getDescription() { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+ string getDescription() { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
-
+ string getDescription() { return "removes gap characters from sequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Deunique.seqs"; }
+ string getDescription() { return "reverse of the unique.seqs command, and creates a fasta file from a fasta and name file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Deunique.tree"; }
+ string getDescription() { return "add the redundant sequence names back into a tree of unique sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
-
+ string getDescription() { return "calculate the pairwaise distances between aligned sequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }\r
string getHelpString(); \r
string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
+ string getDescription() { return "removes columns from alignments based on a criteria defined by the user"; }\r
\r
int execute(); \r
void help() { m->mothurOut(getHelpString()); } \r
}
out << "citation=" << newCitationString << endl;
+ out << "description=" << thisCommand->getDescription() << endl;
+
//outputTypes - makes something like outputTypes=fasta-name-qfile
map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
map<string, vector<string> >::iterator itTypes;
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
+ string getDescription() { return "get.commandinfo"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.current"; }
+ string getDescription() { return "get current files saved by mothur"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.group"; }
+ string getDescription() { return "outputs group names"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
+ string getDescription() { return "gets sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.label"; }
+ string getDescription() { return "outputs labels"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
+ string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandName() { return "get.otulist"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getCitation() { return "http://www.mothur.org/wiki/Get.otulist"; }
+ string getDescription() { return "lists each OTU number and the sequence contained in that OTU"; }
+
string getHelpString();
int execute();
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
+ string getDescription() { return "gets a representative sequence for each OTU"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
+ string getDescription() { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.rabund"; }
+ string getDescription() { return "creates a rabund file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.relabund"; }
+ string getDescription() { return "calculates the relative abundance of each OTU in a sample"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.sabund"; }
-
+ string getDescription() { return "creates a sabund file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
-
+ string getDescription() { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getRequiredCommand() { return "none"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.sharedseqs"; }
-
+ string getDescription() { return "identifies sequences that are either unique or shared by specific groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
-
+ string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.bin"; }
+ string getDescription() { return "generate a heatmap where the color represents the relative abundanceof an OTU"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Heatmap.sim"; }
-
+ string getDescription() { return "generate a heatmap indicating the pairwise distance between multiple samples using a variety of calculators"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "For more information about a specific command type 'commandName(help)' i.e. 'cluster(help)'"; }
string getCitation() { return "no citation"; }
-
+ string getDescription() { return "help"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
-
+ string getDescription() { return "homova"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.\n McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Indicator"; }
-
+ string getDescription() { return "calculate the indicator value for each OTU for each tree node"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
-
+ string getDescription() { return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
-
+ string getDescription() { return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.fastq"; }
+ string getDescription() { return "creates a fastq file from a fasta and quality file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.group"; }
-
+ string getDescription() { return "creates a group file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Mantel"; }
-
+ string getDescription() { return "mantel"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
+ string getDescription() { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Merge.files"; }
+ string getDescription() { return "appends files creating one file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Merge.groups"; }
+ string getDescription() { return "reads shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
-
+ string getDescription() { return "detects differentially abundant features in clinical metagenomic samples"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
-
+ string getDescription() { return "cluster your sequences into OTUs using a blast file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Borg, Groenen (1997). Non-metric multidimensional scaling function using the majorization algorithm, in Modern Multidimensional Scaling. Ed. T.F. Cox and M.A.A. Cox. Chapman and Hall. \nhttp://www.mothur.org/wiki/Nmds"; }
-
+ string getDescription() { return "nmds"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "No Command"; }
string getCitation() { return "no citation"; }
+ string getDescription() { return "no description"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
+ string getDescription() { return "normalize samples in a shared or relabund file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Otu.hierarchy"; }
+ string getDescription() { return "relates OTUs at different distances"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
-
+ string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Parse.fastq"; }
+ string getDescription() { return "reads a fastq file and creates a fasta and quality file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Parse.list"; }
+ string getDescription() { return "parses a list file by group"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
-
+ string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pca"; }
-
+ string getDescription() { return "pca"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Pcoa"; }
-
+ string getDescription() { return "pcoa"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Faith DP (1994). Phylogenetic pattern and the quantification of organismal biodiversity. Philos Trans R Soc Lond B Biol Sci 345: 45-58. \nhttp://www.mothur.org/wiki/Phylo.diversity"; }
-
+ string getDescription() { return "phylo.diversity"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
-
+ string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
+ string getDescription() { return "pat's pipeline"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
+ string getDescription() { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "The quit command will terminate mothur and should be in the following format: quit() or quit. \n"; }
string getCitation() { return "no citation"; }
-
+ string getDescription() { return "quit"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
-
+ string getDescription() { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
-
+ string getDescription() { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; }
string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
-
+ string getDescription() { return "read.dist"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like collect.shared."; }
string getCitation() { return "http://www.mothur.org/wiki/Read.otu"; }
+ string getDescription() { return "read.otu"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }
string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
+ string getDescription() { return "read.tree"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
+ string getDescription() { return "removes sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Phylotype Analysis"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
-
+ string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
-
+ string getDescription() { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
+ string getDescription() { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
-
+ string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Reverse.seqs"; }
+ string getDescription() { return "outputs a fasta file containing the reverse-complements"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Screen.seqs"; }
-
+ string getDescription() { return "enables you to keep sequences that fulfill certain user defined criteria"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+ string getDescription() { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Sens.spec"; }
-
+ string getDescription() { return "sens.spec"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+ string getDescription() { return "seq.error"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+ string getDescription() { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Set.current"; }
-
+ string getDescription() { return "set current files for mothur"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Set.dir"; }
-
+ string getDescription() { return "set input, output and default directories"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Set.logfile"; }
-
+ string getDescription() { return "set logfile name"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
-
+ string getDescription() { return "extract sequences reads from a .sff file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Make.shared"; }
-
+ string getDescription() { return "make a shared file from a list and group file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
+ string getDescription() { return "shhh.seqs"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Split.abund"; }
+ string getDescription() { return "split a list, name, group or fasta file based on abundance"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+ string getDescription() { return "split a name or fasta file by group"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Sub.sample"; }
-
+ string getDescription() { return "get a sampling of sequences from a list, shared, rabund, sabund or fasta file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
+ string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
-
+ string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "General"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/System"; }
-
+ string getDescription() { return "excute system commands from within mothur"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
+ string getDescription() { return "generate a tree file that describes the dissimilarity among groups"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
string getCitation() { return "no citation"; }
+ string getDescription() { return "trim.flows"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
-
+ string getDescription() { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Lozupone C, Knight R (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-35. \nhttp://www.mothur.org/wiki/Unifrac.unweighted"; }
-
+ string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "Hypothesis Testing"; }
string getHelpString();
string getCitation() { return "Lozupone CA, Hamady M, Kelley ST, Knight R (2007). Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-85. \nhttp://www.mothur.org/wiki/Unifrac.weighted"; }
-
+ string getDescription() { return "generic tests that describes whether two or more communities have the same structure"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Venn"; }
-
+ string getDescription() { return "generates a Venn diagram from data provided in a shared file"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
projects / mothur.git / commitdiff