PDS: update citation fields

diff --git a/catchallcommand.h b/catchallcommand.h
index d1b8a2a8dfabf300d4d6cb7591e043e2ea48b113..44ed3ef162b0a82465c1662f2f19e73d43468f86 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -33,7 +33,7 @@ public:
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getOutputFileNameTag(string, string);
        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 getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics  28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
        string getDescription()         { return "estimate number of species"; }
        
        int execute(); 

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 1c4baa3f8f0d5a8b5724af661f51850b6d0b4762..b6957e39d45cc877a9bee28cccf933af6d86f49e 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -30,7 +30,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing"; }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Chimera.perseus\n"; }
+       string getCitation() { return "Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.perseus\n"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index a2e22ae527d465b475a4f89b5fa606198315c3a4..82e1228606986b18d7176a5cdf70e84a83cb695f 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -29,7 +29,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing"; }
        string getOutputFileNameTag(string, string);
        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 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  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 5423a171d5698bda82c5869401e3509e1f059439..3ca79391b5d1280c5b5943ada46599cbc98d44b0 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -28,7 +28,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing"; }
        string getOutputFileNameTag(string, string);
        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\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
+       string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code was donated to the public domain.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.uchime\n"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 

diff --git a/classifyotucommand.h b/classifyotucommand.h
index b924775cf5b30436c1783714a758281cf072c32f..36a0328aa85bb2d646e14ec37b1d13f8a0581241 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -27,7 +27,7 @@ public:
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getOutputFileNameTag(string, string);
        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 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 77:3219.\nhttp://www.mothur.org/wiki/Classify.otu"; }
        string getDescription()         { return "find the concensus taxonomy for each OTU"; }
        
        int execute(); 

diff --git a/clustercommand.h b/clustercommand.h
index f70bb322c76cd3bf897fd5498333e5da379557fd..a5b792ea7c8a3e35345606765aaa3ede84916a86 100644 (file)
--- a/clustercommand.h
+++ b/clustercommand.h
@@ -37,7 +37,7 @@ public:
        string getCommandCategory()             { return "Clustering";  }
        string getOutputFileNameTag(string, string);
        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 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 77:3219.\nSchloss 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"; }
        string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
        
        int execute(); 

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
index ec2f083e987e47f3125f381bd0c1199307dbdaf8..09ee8229984a488f5eeecbcf269922a01c5d9500 100644 (file)
--- a/clusterdoturcommand.h
+++ b/clusterdoturcommand.h
@@ -29,7 +29,7 @@ public:
        string getCommandCategory()             { return "Clustering";                  }
     string getOutputFileNameTag(string, string);
        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 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 77:3219.\nSchloss 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\n";}
        string getDescription()         { return "cluster your sequences into OTUs using DOTUR’s method"; }
        
        int execute(); 

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index d46bb8ed9be115e229cd1ed0ea39a993aa6f61f0..59039ea8600a4ac7e4ea30ab2a684679f6c9f51e 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -37,7 +37,7 @@ public:
        string getCommandCategory()             { return "Clustering";                  }
        string getOutputFileNameTag(string, string);
        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 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 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
        string getDescription()         { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
        
        int execute(); 

diff --git a/cooccurrencecommand.h b/cooccurrencecommand.h
index 530db9e2d27cad41cda6dc4f37ad07b01c570009..08209190f3f51b0e334706530afed253684eb75e 100644 (file)
--- a/cooccurrencecommand.h
+++ b/cooccurrencecommand.h
@@ -30,7 +30,7 @@ public:
        string getCommandCategory()             { return "Hypothesis Testing";  }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Cooccurrence"; }
+       string getCitation() { return "Ulrich W & Gotelli NJ (2010).  Null model analysis of species associations using abundance data.  Ecology  91:3384.\nhttp://www.mothur.org/wiki/Cooccurrence"; }
        string getDescription()         { return "calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance."; }
        
        int execute(); 

diff --git a/pipelinepdscommand.h b/pipelinepdscommand.h
index 2c621bbe1da5b94bf9dd13f40d97bd27ef7b7c97..4697f405f6045cabad7f225641c4544a36ca6e9f 100644 (file)
--- a/pipelinepdscommand.h
+++ b/pipelinepdscommand.h
@@ -28,7 +28,7 @@ public:
        string getCommandCategory()             { return "Hidden";                      }
        string getOutputFileNameTag(string, string) { return ""; }
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Pipeline.pds"; }
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Pipeline.pds"; }
        string getDescription()         { return "pat's pipeline"; }
 
        

diff --git a/preclustercommand.h b/preclustercommand.h
index 084bdc61ee464c665e2f37e200b38c09b85e8ef6..082bff27e25209fc7db92404388ae40592d45bff 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -43,7 +43,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing";         }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Pre.cluster"; }
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://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"; }
 
        

diff --git a/sensspeccommand.h b/sensspeccommand.h
index a5072e80c4bd908ed63d0f1ab34c83a5285b2e95..be5e975f0d6b6bc33db2d40564a6ca5df3b08703 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -28,7 +28,7 @@ public:
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getOutputFileNameTag(string, string);
        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 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 77:3219.\nhttp://www.mothur.org/wiki/Sens.spec"; }
        string getDescription()         { return "sens.spec"; }
 
        int execute(); 

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 660544fff2982a325c325932b3972d9b3451f3c4..fba392d800a1f2454310ff57904a40454b231fd4 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -26,7 +26,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing";         }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
        string getDescription()         { return "seq.error"; }
 
        

diff --git a/shhhercommand.h b/shhhercommand.h
index 03f171e8a85cf0ebe363381793fbaea7e69950ab..8446444bcc23d1f0548cfe2c2d2cfc9868467434 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -43,7 +43,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing";         }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Shhh.flows"; }
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nQuince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009).  Accurate determination of microbial diversity from 454 pyrosequencing data.  Nat. Methods 6:639.\nhttp://www.mothur.org/wiki/Shhh.flows"; }
        string getDescription()         { return "shhh.flows"; }
 
        

diff --git a/shhhseqscommand.h b/shhhseqscommand.h
index a4695be5934eddf0fab5da392fe587b1a8199432..85be58c307e8a425e9ac4de4b7c2a99e3fe201d7 100644 (file)
--- a/shhhseqscommand.h
+++ b/shhhseqscommand.h
@@ -31,7 +31,7 @@ public:
        string getCommandCategory()             { return "Sequence Processing";         }
        string getOutputFileNameTag(string, string);
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Shhh.seqs"; }
+       string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011).  Removing noise from pyrosequenced amplicons.  BMC Bioinformatics  12:38.\nhttp://www.mothur.org/wiki/Shhh.seqs"; }
        string getDescription()         { return "shhh.seqs"; }