Merge remote-tracking branch 'origin/master'

diff --git a/.gitignore b/.gitignore
index c1f854e3d6c22d93a5a03c0e365c472a1da46d68..ac6f4409bf8be051d0665c0743bf853f42579f25 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 .DS_Store
 *.zip
+*.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index b2895e8b73839ec48b795ab0877b0e9aad0eb330..ecb0619a39d993201f9bd102813c9b10b7cc3f0b 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2294,7 +2294,7 @@
                                DEPLOYMENT_LOCATION = YES;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                PRODUCT_NAME = mothur;
                                SDKROOT = macosx10.6;
                                SKIP_INSTALL = NO;
@@ -2308,6 +2308,7 @@
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                DEPLOYMENT_LOCATION = YES;
                                GCC_MODEL_TUNING = G5;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
                                PRODUCT_NAME = mothur;
                                SKIP_INSTALL = NO;
@@ -2323,7 +2324,7 @@
                                GCC_ENABLE_SSE3_EXTENSIONS = NO;
                                GCC_ENABLE_SSE41_EXTENSIONS = NO;
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
                                        "VERSION=\"\\\"1.26.0\\\"\"",
@@ -2360,7 +2361,7 @@
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "VERSION=\"\\\"1.27.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"8/8/2012\\\"\"",

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 3608835cd16ed30f648469f308d2320f23bf423e..e2855d019ff984d9ac026a2554860c5b3aa33f42 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -32,7 +32,7 @@ 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 93adb7bf53b280892715411c66aedcf15b5c0df3..4d53c5c048dafe1f969437a384ea93a160a83c04 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -30,7 +30,7 @@ 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 a5b42751dfd74ea3eb1fc3dc4ccf9bfa5bb9822b..f0c30d08a03f1834de06c550668e6b3b1f64c1b1 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -30,7 +30,7 @@ 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 45e377c3cbe1ac1ad735cd9c4f47d4c4c37c30a5..2e76057f1219b8c44785a5be9b6962043bbb68af 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -28,7 +28,7 @@ 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 0f8657c6236baf9554a136b464118d9104b6dc93..dd61a35bdcf3e45a72a590ec9b430584cc30376d 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 e079197c1ea60d15e2454ad7433e90d2cfbbc611..936ae6f69ce94877b60b9f99219423db8b526d73 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 9844b8ffc1a951c47d606ec23e7caf45b4bf4ce1..e63afa6c8af8ee442e267714fcfccd140d4f79dd 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -50,7 +50,7 @@ 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 9820ccef15f6db94747913eda42e468dba771064..ef52dcd1d761cb26d67bb3c8556e7358c3d57440 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -42,7 +42,7 @@ 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"; }