https://beikolab.cs.dal.ca/software/api.php?action=feedcontributions&user=Mporter&feedformat=atomBioinformatics Software - User contributions [en]2024-03-28T13:12:20ZUser contributionsMediaWiki 1.34.0https://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1122SPANNER2013-04-03T09:49:01Z<p>Mporter: /* Obtaining the Software */</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install SPANNER under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
Reference LCA Profiles are also available as a gzipped tarball. These LCA Profiles can be used as a reference dataset by SPANNER and were created from an all-versus-all BLASTp of nr at an e-value threshold of 0.01. These profiles will be updated as new versions of nr are released; the version used here was obtained from ncbi in March 2013. Note: this file is 5 GB in size, uncompressed it is 20 GB.<br />
<br />
* [http://kiwi.cs.dal.ca/~mikep/ReferencenrLCAProfiles.tar.gz Reference nr LCA Profiles v03.2013]<br />
<br />
Full instructions on using these reference LCA Profiles can be found in the README.txt file inside the tarball. Brief instructions for using these Profiles:<br />
<br />
* These Profiles have not been trimmed to any ''p'' value, but instead include all BLASTp matches. In the SPANNER paper the reference Profiles were trimmed to the same ''p'' value as the query Profiles. The SPANNER tarball contains the Python script "trim_profiles_to_p.py" in the SCRIPTS directory to remove matches below a given ''p'' value. Running this script on the reference Profiles will greatly reduce the size of the reference dataset.<br />
<br />
* In the SPANNER paper only the highest BLASTp match to any taxon was kept in a Profile, subsequent matches were removed. This was not done for these Profiles. The Python script "make_profiles_taxa_singletons.py" (also in the SCRIPTS directory) removes subsequent matches to already matched taxa, this script will reduce the size of the reference Profile dataset but is not necessary.<br />
<br />
* The SPANNER paper also removed LCA Profiles with only one match, this was not done for these Profiles. The tarball contains the Python script "remove_singletons_from_profiles.py" in the SCRIPTS directory. This script should be run after "make_profiles_taxa_singletons.py" but again is not necessary for SPANNER to function. Reference Profiles with only one match should be removed if query profiles with only one match are removed (those query profiles should be classified using Best BLAST instead).<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.beem.utoronto.ca BEEM (Bioproducts + Enzymes from Environmental Metagenomes)]<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1121SPANNER2013-04-03T02:35:37Z<p>Mporter: /* Obtaining the Software */</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install SPANNER under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
Reference LCA Profiles are also available as a gzipped tarball. These LCA Profiles can be used as a reference dataset by SPANNER and were created from an all-versus-all BLASTp of nr at an e-value threshold of 0.01. These profiles will be updated as new versions of nr are released; the version used here was obtained from ncbi in March 2013.<br />
<br />
* [[Media:referencenrLCAProfiles.tar.gz|Reference nr LCA Profiles v03.2013]]<br />
<br />
Full instructions on using these reference LCA Profiles can be found in the README.txt file inside the tarball. Brief instructions for using these Profiles:<br />
<br />
* These Profiles have not been trimmed to any ''p'' value, but instead include all BLASTp matches. In the SPANNER paper the reference Profiles were trimmed to the same ''p'' value as the query Profiles. The SPANNER tarball contains the Python script "trim_profiles_to_p.py" in the SCRIPTS directory to remove matches below a given ''p'' value. Running this script on the reference Profiles will greatly reduce the size of the reference dataset.<br />
<br />
* In the SPANNER paper only the highest BLASTp match to any taxon was kept in a Profile, subsequent matches were removed. This was not done for these Profiles. The Python script "make_profiles_taxa_singletons.py" (also in the SCRIPTS directory) removes subsequent matches to already matched taxa, this script will reduce the size of the reference Profile dataset but is not necessary.<br />
<br />
* The SPANNER paper also removed LCA Profiles with only one match, this was not done for these Profiles. The tarball contains the Python script "remove_singletons_from_profiles.py" in the SCRIPTS directory. This script should be run after "make_profiles_taxa_singletons.py" but again is not necessary for SPANNER to function. Reference Profiles with only one match should be removed if query profiles with only one match are removed (those query profiles should be classified using Best BLAST instead).<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.beem.utoronto.ca BEEM (Bioproducts + Enzymes from Environmental Metagenomes)]<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1120SPANNER2013-04-03T02:35:24Z<p>Mporter: /* Obtaining the Software */</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install the SPANNER under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
Reference LCA Profiles are also available as a gzipped tarball. These LCA Profiles can be used as a reference dataset by SPANNER and were created from an all-versus-all BLASTp of nr at an e-value threshold of 0.01. These profiles will be updated as new versions of nr are released; the version used here was obtained from ncbi in March 2013.<br />
<br />
* [[Media:referencenrLCAProfiles.tar.gz|Reference nr LCA Profiles v03.2013]]<br />
<br />
Full instructions on using these reference LCA Profiles can be found in the README.txt file inside the tarball. Brief instructions for using these Profiles:<br />
<br />
* These Profiles have not been trimmed to any ''p'' value, but instead include all BLASTp matches. In the SPANNER paper the reference Profiles were trimmed to the same ''p'' value as the query Profiles. The SPANNER tarball contains the Python script "trim_profiles_to_p.py" in the SCRIPTS directory to remove matches below a given ''p'' value. Running this script on the reference Profiles will greatly reduce the size of the reference dataset.<br />
<br />
* In the SPANNER paper only the highest BLASTp match to any taxon was kept in a Profile, subsequent matches were removed. This was not done for these Profiles. The Python script "make_profiles_taxa_singletons.py" (also in the SCRIPTS directory) removes subsequent matches to already matched taxa, this script will reduce the size of the reference Profile dataset but is not necessary.<br />
<br />
* The SPANNER paper also removed LCA Profiles with only one match, this was not done for these Profiles. The tarball contains the Python script "remove_singletons_from_profiles.py" in the SCRIPTS directory. This script should be run after "make_profiles_taxa_singletons.py" but again is not necessary for SPANNER to function. Reference Profiles with only one match should be removed if query profiles with only one match are removed (those query profiles should be classified using Best BLAST instead).<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.beem.utoronto.ca BEEM (Bioproducts + Enzymes from Environmental Metagenomes)]<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1119SPANNER2013-03-26T12:42:20Z<p>Mporter: /* Obtaining the Software */</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install the FCP under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
Reference LCA Profiles are also available as a gzipped tarball. These LCA Profiles can be used as a reference dataset by SPANNER and were created from an all-versus-all BLASTp of nr at an e-value threshold of 0.01. These profiles will be updated as new versions of nr are released; the version used here was obtained from ncbi in March 2013.<br />
<br />
* [[Media:referencenrLCAProfiles.tar.gz|Reference nr LCA Profiles v03.2013]]<br />
<br />
Full instructions on using these reference LCA Profiles can be found in the README.txt file inside the tarball. Brief instructions for using these Profiles:<br />
<br />
* These Profiles have not been trimmed to any ''p'' value, but instead include all BLASTp matches. In the SPANNER paper the reference Profiles were trimmed to the same ''p'' value as the query Profiles. The SPANNER tarball contains the Python script "trim_profiles_to_p.py" in the SCRIPTS directory to remove matches below a given ''p'' value. Running this script on the reference Profiles will greatly reduce the size of the reference dataset.<br />
<br />
* In the SPANNER paper only the highest BLASTp match to any taxon was kept in a Profile, subsequent matches were removed. This was not done for these Profiles. The Python script "make_profiles_taxa_singletons.py" (also in the SCRIPTS directory) removes subsequent matches to already matched taxa, this script will reduce the size of the reference Profile dataset but is not necessary.<br />
<br />
* The SPANNER paper also removed LCA Profiles with only one match, this was not done for these Profiles. The tarball contains the Python script "remove_singletons_from_profiles.py" in the SCRIPTS directory. This script should be run after "make_profiles_taxa_singletons.py" but again is not necessary for SPANNER to function. Reference Profiles with only one match should be removed if query profiles with only one match are removed (those query profiles should be classified using Best BLAST instead).<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.beem.utoronto.ca BEEM (Bioproducts + Enzymes from Environmental Metagenomes)]<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=File:SPANNER.tar.gz&diff=1089File:SPANNER.tar.gz2012-12-18T18:10:51Z<p>Mporter: v1.0.0; initial release</p>
<hr />
<div>v1.0.0; initial release</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1088SPANNER2012-12-18T01:49:32Z<p>Mporter: /* Funding */</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install the FCP under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.beem.utoronto.ca BEEM (Bioproducts + Enzymes from Environmental Metagenomes)]<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1087SPANNER2012-12-18T00:27:25Z<p>Mporter: </p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install the FCP under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=SPANNER&diff=1086SPANNER2012-12-18T00:24:29Z<p>Mporter: New page: __NOTOC__ SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments. == License == This software is releas...</p>
<hr />
<div>__NOTOC__<br />
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.<br />
<br />
== License ==<br />
<br />
This software is released under the [http://www.gnu.org/licenses/gpl.html GNU General Public License v3.0].<br />
<br />
== Obtaining the Software ==<br />
<br />
SPANNER is available as a gzipped tarball, supported on *nix systems (Linux, Unix, Mac).<br />
<br />
* [[Media:SPANNER.tar.gz|SPANNER v1.0.0 (gzipped tarball)]]<br />
<br />
After downloading, uncompress the file and follow the installation instructions in the INSTALL.txt file. Additional instructions are located in the README.txt and MANUAL.txt files. To install the FCP under OS X, gcc must be installed which is available as part of the [http://developer.apple.com/technologies/tools/ Mac Developer Tools].<br />
<br />
== Citing SPANNER ==<br />
<br />
If you find this software helpful in your research, please cite:<br />
<br />
* '''Porter, M.S., Beiko, R.G. SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles. ''Submitted to BMC Bioinformatics''.'''<br />
<br />
== Contact Information ==<br />
<br />
SPANNER is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Version History ==<br />
<br />
''v1.0.0 (December 17, 2012)''<br />
* initial software release.<br />
<br />
== Funding ==<br />
<br />
The development of this software has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Canadian Foundation for Innovation<br />
* Genome Canada<br />
* Ontario Genomics Institute</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=Main_Page&diff=1085Main Page2012-12-18T00:14:06Z<p>Mporter: /* Software (Currently Supported) */</p>
<hr />
<div>__NOTOC__<br />
[[Image:GenGIS_galapagos.jpg|frame|right|Using GenGIS to investigate the distribution of photorhodopsin genes around the Galapagos Islands (data courtesy of Adrian Sharma, Jeremy Koenig, and Olga Zhaxybayeva).]]<br />
<br />
Welcome to the Bioinformatics Software and Resources page.<br />
<br />
== Software (Currently Supported) ==<br />
Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer, A = sequence alignment<br />
<br />
* [http://bioinformatics.org.au/evolsim/ EvolSimulator]: a simulation test bed for hypotheses of genome evolution. (PL)<br />
<br />
* [[ExpressBetaDiversity | Express Beta Diversity (EBD)]]: taxon- and phylogenetic-based beta diversity measures. (P)<br />
<br />
* [[FCP | Fragment classification package (FCP)]]: Homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments. (GML)<br />
<br />
* [http://kiwi.cs.dal.ca/GenGIS GenGIS]: an application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. (PSBVM)<br />
<br />
* [[NetworkDiversity| Network Diversity]]: calculation of beta diversity over phylogenetic networks. (P)<br />
<br />
* [[RITA]]: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).<br />
<br />
* [http://kiwi.cs.dal.ca/Software/rSPR rSPR]: software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests. (PL)<br />
<br />
* [[SPANNER]]: Homology-based taxonomic classification of protein sequences. (GML)<br />
<br />
* [[SPRSupertrees]]: software to calculate rooted supertrees that minimize the SPR distance. (PL)<br />
<br />
* [[STAMP]]: a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. (SMV)<br />
<br />
== Older Software ==<br />
<br />
The following software packages have largely been superseded by others in the above list, or by software written by others. The software should still work, but we can no longer offer significant support for it.<br />
<br />
* [http://bioinformatics.org.au/eeep/ EEEP (Efficient Evaluation of Edit Paths)]: software to infer putative pathways of lateral genetic transfer by comparing gene trees against a rooted reference tree (PL)<br />
<br />
* [[PICA]]: genotype-phenotype data mining software (G).<br />
<br />
* [http://kiwi.cs.dal.ca/~beiko/software-and-data/radie Radié]: a tool that allows characters to be visualized against the background of a phylogenetic tree. The software includes several different visual and numeric representations of the ‘convexity’ of a given character, in other words the extent to which different character traits form distinct groups within the tree. (PV)<br />
<br />
* [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation in mind.<br />
<br />
* [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (SA)<br />
<br />
== Web Services ==<br />
* [http://ratite.cs.dal.ca/SeqMonitor SeqMonitor]<br />
* [http://bio.mquter.qut.edu.au/Moa/ MOAMap]<br />
* [http://fester.cs.dal.ca/manuel MANUEL]<br />
<br />
== Mailing list ==<br />
<br />
* Join our [http://ratite.cs.dal.ca/software_email_list/subscribe mailing list] to keep informed about new developments.<br />
<br />
== Datasets ==<br />
* [http://kiwi.cs.dal.ca/GenGIS/Datasets Datasets used in GenGIS] (Parks et al., Genome Research 2009)<br />
* [http://kiwi.cs.dal.ca/Software/STAMP_example_datasets STAMP datasets]<br />
* [http://bioinformatics.org.au/lgt144/ Lateral genetic transfer in 144 genomes dataset] (Beiko et al., Proc. Natl. Acad. Sci. 2005)<br />
* Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008) [to be added]<br />
<br />
== Contributors ==<br />
* [http://kiwi.cs.dal.ca/~beiko/ Robert Beiko]<br />
* [http://www.cs.dal.ca/~cblouin Christian Blouin]<br />
* [http://dparks.wikidot.com/ Donovan Parks]<br />
* [http://www.cs.dal.ca/~whidden Chris Whidden]<br />
* Norman MacDonald</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=STAMP&diff=530STAMP2010-05-18T15:35:08Z<p>Mporter: /* Downloads */</p>
<hr />
<div>__NOTOC__<br />
[[Image:StampIcon.png|left]]<br />
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]<br />
<br />
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.<br />
<br />
=== Announcements ===<br />
<br />
* May 18, 2010: STAMP v1.05 released. Minor bug fixes.<br />
* April 16, 2010: STAMP v1.04 released. Fixes bug which caused the ordering of labels to be reversed in extended error plots (bug introduced in v1.02). <br />
* April 12, 2010: STAMP v1.03 released. Fixes bug which prevented tables from being saved.<br />
<br />
=== Mailing list ===<br />
<br />
* Join our [http://ratite.cs.dal.ca/software_email_list/subscribe mailing list] to keep informed about STAMP developments.<br />
<br />
=== Documentation ===<br />
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)<br />
* [[Media:STAMP_Users_Guide.pdf|User's Guide]]<br />
* [[STAMP FAQs|FAQs]]<br />
* [[STAMP version history|Version history]]<br />
<br />
=== Downloads ===<br />
* [[Media:STAMP_1.05_Setup.exe|STAMP v1.05 executable]] for Microsoft Windows (~17MB)<br />
* [[Media:STAMP_1_05_Max_OSX.zip|STAMP v1.05 executable]] for Mac OS X Leopard and Snow Leopard (~72MB) [Beta version: if you experience problems please let us know.]<br />
* [[Media:STAMP_1_05_source.zip|STAMP v1.05 source code]]<br />
<br />
=== Examples ===<br />
* [[STAMP image gallery|Image gallery]]<br />
* [[STAMP example datasets|Example datasets]]<br />
<br />
== Citing STAMP ==<br />
<br />
If you use STAMP in your research, please cite:<br />
<br />
'''Parks, D.H. and Beiko, R.G. (2010). Identifying biologically relevant differences between metagenomic communities. ''Bioinformatics'', 26, 715-721.''' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Abstract])<br />
<br />
== Contact Information ==<br />
<br />
STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Funding ==<br />
<br />
The development and deployment of STAMP has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]<br />
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]<br />
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=File:STAMP_1_05_Max_OSX.zip&diff=529File:STAMP 1 05 Max OSX.zip2010-05-18T15:34:44Z<p>Mporter: </p>
<hr />
<div></div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=File:STAMP_1_01_Mac_OSX.zip&diff=456File:STAMP 1 01 Mac OSX.zip2010-03-10T15:19:52Z<p>Mporter: uploaded a new version of "Image:STAMP 1 01 Mac OSX.zip"</p>
<hr />
<div>STAMP v1.01 for Apple's Mac OSX.</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=STAMP&diff=445STAMP2010-02-22T13:50:51Z<p>Mporter: /* Downloads */</p>
<hr />
<div>__NOTOC__<br />
[[Image:StampIcon.png|left]]<br />
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]<br />
<br />
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.<br />
<br />
=== Documentation ===<br />
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)<br />
* [[Media:STAMP_Users_Guide.pdf|User's Guide]]<br />
* [[STAMP FAQs|FAQs]]<br />
* [[STAMP version history|Version history]]<br />
<br />
=== Downloads ===<br />
* [[Media:STAMP_1.01_Setup.exe|STAMP v1.01 executable]] for Microsoft Windows (~17MB)<br />
* [[Media:STAMP_1_01_Mac_OSX.zip|STAMP v1.01 executable]] for Mac OS X Leopard and Snow Leopard (~72MB) (The Mac version is a work in progress, let us know if there are any problems with it. If it doesn't work STAMP can still be built for the Mac from the source code, see instructions [[Quick installation instructions for STAMP#Source code on Apple.27s OS X|here]].)<br />
* [[Media:STAMP_1_01_source.zip|STAMP v1.01 source code]]<br />
<br />
=== Examples ===<br />
* [[STAMP image gallery|Image gallery]]<br />
* [[STAMP example datasets|Example datasets]]<br />
<br />
== Citing STAMP ==<br />
<br />
If you use STAMP in your research, please cite:<br />
<br />
'''Parks, D.H. and Beiko, R.G. ''Identifying biologically relevant differences between metagenomic communities.'' Submitted to Bioinformatics on Dec. 11, 2009.'''<br />
<br />
== Contact Information ==<br />
<br />
STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Funding ==<br />
<br />
The development and deployment of STAMP has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]<br />
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]<br />
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=STAMP&diff=444STAMP2010-02-22T13:49:43Z<p>Mporter: /* Downloads */</p>
<hr />
<div>__NOTOC__<br />
[[Image:StampIcon.png|left]]<br />
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]<br />
<br />
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.<br />
<br />
=== Documentation ===<br />
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)<br />
* [[Media:STAMP_Users_Guide.pdf|User's Guide]]<br />
* [[STAMP FAQs|FAQs]]<br />
* [[STAMP version history|Version history]]<br />
<br />
=== Downloads ===<br />
* [[Media:STAMP_1.01_Setup.exe|STAMP v1.01 executable]] for Microsoft Windows (~17MB)<br />
* [[Media:STAMP_1_01_Mac_OSX.zip|STAMP v1.01 executable]] for Mac OS X Leopard and Snow Leopard (The Mac version is a work in progress, let us know if there are any problems with it. If it doesn't work STAMP can still be built for the Mac from the source code, see instructions [[Quick installation instructions for STAMP#Source code on Apple.27s OS X|here]].)<br />
* [[Media:STAMP_1_01_source.zip|STAMP v1.01 source code]]<br />
<br />
=== Examples ===<br />
* [[STAMP image gallery|Image gallery]]<br />
* [[STAMP example datasets|Example datasets]]<br />
<br />
== Citing STAMP ==<br />
<br />
If you use STAMP in your research, please cite:<br />
<br />
'''Parks, D.H. and Beiko, R.G. ''Identifying biologically relevant differences between metagenomic communities.'' Submitted to Bioinformatics on Dec. 11, 2009.'''<br />
<br />
== Contact Information ==<br />
<br />
STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Funding ==<br />
<br />
The development and deployment of STAMP has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]<br />
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]<br />
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=File:STAMP_1_01_Mac_OSX.zip&diff=443File:STAMP 1 01 Mac OSX.zip2010-02-22T13:45:27Z<p>Mporter: uploaded a new version of "Image:STAMP 1 01 Mac OSX.zip"</p>
<hr />
<div>STAMP v1.01 for Apple's Mac OSX.</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=File:STAMP_1_01_Mac_OSX.zip&diff=441File:STAMP 1 01 Mac OSX.zip2010-02-10T00:51:59Z<p>Mporter: uploaded a new version of "Image:STAMP 1 01 Mac OSX.zip"</p>
<hr />
<div>STAMP v1.01 for Apple's Mac OSX.</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=STAMP&diff=440STAMP2010-02-05T00:27:06Z<p>Mporter: /* Downloads */</p>
<hr />
<div>__NOTOC__<br />
[[Image:StampIcon.png|left]]<br />
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]<br />
<br />
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.<br />
<br />
=== Documentation ===<br />
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)<br />
* [[Media:STAMP_Users_Guide.pdf|User's Guide]]<br />
* [[STAMP FAQs|FAQs]]<br />
* [[STAMP version history|Version history]]<br />
<br />
=== Downloads ===<br />
* [[Media:STAMP_1.01_Setup.exe|STAMP v1.01 executable]] for Microsoft Windows (~17MB)<br />
* [[Media:STAMP_1_01_source.zip|STAMP v1.01 source code]]<br />
<br />
=== Examples ===<br />
* [[STAMP image gallery|Image gallery]]<br />
* [[STAMP example datasets|Example datasets]]<br />
<br />
== Citing STAMP ==<br />
<br />
If you use STAMP in your research, please cite:<br />
<br />
'''Parks, D.H. and Beiko, R.G. ''Identifying biologically relevant differences between metagenomic communities.'' Submitted to Bioinformatics on Dec. 11, 2009.'''<br />
<br />
== Contact Information ==<br />
<br />
STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Funding ==<br />
<br />
The development and deployment of STAMP has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]<br />
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]<br />
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]</div>Mporterhttps://beikolab.cs.dal.ca/software/index.php?title=STAMP&diff=439STAMP2010-02-04T23:15:09Z<p>Mporter: /* Downloads */</p>
<hr />
<div>__NOTOC__<br />
[[Image:StampIcon.png|left]]<br />
[[Image:RumenErrorBarPlot.png|thumb|right|500px|Using STAMP to identify SEED subsystems which are differentially abundant in a pair of bovine rumen microbiomes (data originally described in [http://www.ncbi.nlm.nih.gov/pubmed/19181843 Brulc et al., 2009]).]]<br />
<br />
STAMP ('''St'''atistical '''A'''nalysis of '''M'''etagenomic '''P'''rofiles) is a software package for analyzing metagenomic profiles (e.g., a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open source, extensible via a plugin framework, and available for all major platforms.<br />
<br />
=== Documentation ===<br />
* [[Quick installation instructions for STAMP|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)<br />
* [[Media:STAMP_Users_Guide.pdf|User's Guide]]<br />
* [[STAMP FAQs|FAQs]]<br />
* [[STAMP version history|Version history]]<br />
<br />
=== Downloads ===<br />
* [[Media:STAMP_1.01_Setup.exe|STAMP v1.01 executable]] for Microsoft Windows (~17MB)<br />
* [[Media:STAMP_1_01_source.zip|STAMP v1.01 source code]]<br />
* [[Media:STAMP_1_01_mac.zip|STAMP v1.01 executable]] for Mac OS 10.5 or 10.6 (~112MB)<br />
<br />
=== Examples ===<br />
* [[STAMP image gallery|Image gallery]]<br />
* [[STAMP example datasets|Example datasets]]<br />
<br />
== Citing STAMP ==<br />
<br />
If you use STAMP in your research, please cite:<br />
<br />
'''Parks, D.H. and Beiko, R.G. ''Identifying biologically relevant differences between metagenomic communities.'' Submitted to Bioinformatics on Dec. 11, 2009.'''<br />
<br />
== Contact Information ==<br />
<br />
STAMP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue. <br />
<br />
== Funding ==<br />
<br />
The development and deployment of STAMP has been supported by several organizations:<br />
<br />
* [http://www.genomeatlantic.ca Genome Atlantic]<br />
* The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the [http://www.tula.org/ Tula Foundation]<br />
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]<br />
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]</div>Mporter