Difference between revisions of "RSPR"

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(New page: rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests. === Documentation === * [[Quick installation instructions for rSPR|Quic...)
 
(Citing rSPR)
 
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rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests.
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__NOTOC__
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rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests. Version 1.2.0 includes an implementation of the cluster reduction and edge protection and is significantly faster than the previous versions in many cases.
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rSPR is available as C++ source code under the GNU GPL v3.
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This is free software, and you are welcome to redistribute it
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under certain conditions; See the README for details.
  
 
=== Documentation ===
 
=== Documentation ===
* [[Quick installation instructions for rSPR|Quick installation instructions]] (Microsoft Windows, Apple's Mac OS X, Command-line interface)
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* [[rSPR README|README]]
* [[Media:rSPR_Users_Guide.pdf|User's Guide]]
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* [[rSPR FAQs|FAQs]]
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* [[rSPR version history|Version history]]
 
* [[rSPR version history|Version history]]
  
 
=== Downloads ===
 
=== Downloads ===
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* [[Media:rspr_1_3_0_source.zip|rspr v1.3.0 source code]]
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* [[Media:rspr_1_2_1_source.zip|rspr v1.2.1 source code]]
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* [[Media:rspr_1_2_0_source.zip|rspr v1.2.0 source code]]
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* [[Media:rspr_1_1_1_source.zip|rspr v1.1.1 source code]]
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* [[Media:rspr_1_1_0_source.zip|rspr v1.1.0 source code]]
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* [[Media:rspr_1_03_source.zip|rspr v1.03 source code]]
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* [[Media:rspr_1_02_source.zip|rspr v1.02 source code]]
 
* [[Media:rspr_1_01_source.zip|rspr v1.01 source code]]
 
* [[Media:rspr_1_01_source.zip|rspr v1.01 source code]]
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* [[Media:rspr_1_00_source.zip|rspr v1.00 source code]]
  
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<!--
 
=== Examples ===
 
=== Examples ===
 
* [[rSPR example datasets|Example datasets]]
 
* [[rSPR example datasets|Example datasets]]
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-->
  
 
== Citing rSPR ==
 
== Citing rSPR ==
  
If you use STAMP in your research, please cite:
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If you use rSPR in your research, please cite:
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'''Whidden, C., Zeh, N., Beiko, R.G.  ''Computing the SPR Distance of Binary Rooted Trees in O(2^k n) Time''. 2014.''' (In Preparation).
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'''Whidden, C., Zeh, N., Beiko, R.G.  ''Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees''. 2014.''' (In Preparation). ([http://arxiv.org/abs/1305.0512 Preprint])
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'''Whidden, C., Zeh, N., Beiko, R.G. ''Supertrees based on the subtree prune-and-regraft distance''. 2014. Systematic Biology.''' 63 (4), 566-581. doi:10.1093/sysbio/syu023
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'''Whidden, C., Beiko, R.G., Zeh, N. ''Fixed-parameter Algorithms for Maximum Agreement Forests''. SIAM Journal on Computing 42.4 (2013), pp. 1431-1466.''' ([http://epubs.siam.org/doi/abs/10.1137/110845045 Abstract])
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'''Whidden, C., Beiko, R.G., Zeh, N. ''Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments''. In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010)''' ([http://www.springerlink.com/content/e258126735q160q2/ Abstract])
  
'''Whidden, C., Beiko, R.G., Zeh, N. ''Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments (Extended Abstract)'' Accepted to SEA 2010.''' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Abstract])
 
'''Whidden, C. and Zeh, N. ''A Unifying View on Approximation and FPT of Agreement Forests'' Accepted to SEA 2010.''' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/6/715 Abstract])
 
 
'''Whidden, C., Zeh, N. ''A Unifying View on Approximation and FPT of Agreement Forests''. In: WABI 2009. LNCS, vol. 5724, pp. 390–401. Springer-Verlag (2009)''' ([http://www.springerlink.com/content/n56q2846v645p655/ Abstract])
 
'''Whidden, C., Zeh, N. ''A Unifying View on Approximation and FPT of Agreement Forests''. In: WABI 2009. LNCS, vol. 5724, pp. 390–401. Springer-Verlag (2009)''' ([http://www.springerlink.com/content/n56q2846v645p655/ Abstract])
  
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== Funding ==
 
== Funding ==
 
The development of rSPR has been supported by several organizations:
 
  
 
* [http://www.genomeatlantic.ca Genome Atlantic]
 
* [http://www.genomeatlantic.ca Genome Atlantic]
 
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]
 
* [http://www.nserc.ca The Natural Sciences and Engineering Research Council of Canada]
 
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]
 
* The Dalhousie [http://cs.dal.ca Faculty of Computer Science]
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* [http://www.killamtrusts.ca/ The Killam Trusts]
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* [http://www.innovation.ca/ The Canada Foundation for Innovation]
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* [http://www.tula.org/ The Tula Foundation]

Latest revision as of 18:22, 18 June 2014

rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests. Version 1.2.0 includes an implementation of the cluster reduction and edge protection and is significantly faster than the previous versions in many cases.

rSPR is available as C++ source code under the GNU GPL v3. This is free software, and you are welcome to redistribute it under certain conditions; See the README for details.

Documentation

Downloads


Citing rSPR

If you use rSPR in your research, please cite:

Whidden, C., Zeh, N., Beiko, R.G. Computing the SPR Distance of Binary Rooted Trees in O(2^k n) Time. 2014. (In Preparation).

Whidden, C., Zeh, N., Beiko, R.G. Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees. 2014. (In Preparation). (Preprint)

Whidden, C., Zeh, N., Beiko, R.G. Supertrees based on the subtree prune-and-regraft distance. 2014. Systematic Biology. 63 (4), 566-581. doi:10.1093/sysbio/syu023

Whidden, C., Beiko, R.G., Zeh, N. Fixed-parameter Algorithms for Maximum Agreement Forests. SIAM Journal on Computing 42.4 (2013), pp. 1431-1466. (Abstract)

Whidden, C., Beiko, R.G., Zeh, N. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In: Proceedings of the 9th International Symposium on Experimental Algorithms, SEA 2010. Lecture Notes in Computer Science, vol. 6049, pp. 141–153. Springer-Verlag (2010) (Abstract)

Whidden, C., Zeh, N. A Unifying View on Approximation and FPT of Agreement Forests. In: WABI 2009. LNCS, vol. 5724, pp. 390–401. Springer-Verlag (2009) (Abstract)

Contact Information

rSPR 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 Chris Whidden (whidden [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.

Funding