RSPR - Revision history

Cwhidden: /* Citing rSPR */

2014-06-18T18:22:02Z

Citing rSPR

2014-04-30T00:07:14Z

2014-04-30T00:03:39Z

2014-04-30T00:02:59Z

2014-04-29T23:05:38Z

Citing rSPR

2014-04-29T22:47:02Z

Documentation

2014-04-29T22:41:50Z

2014-04-29T22:36:23Z

2014-03-03T21:48:55Z

Downloads

2013-07-26T20:41:12Z

@@ Line 35: / Line 35: @@
 '''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])
-'''Whidden, C., Zeh, N., Beiko, R.G. ''Supertrees based on the subtree prune-and-regraft distance''. 2014. Systematic Biology.''' Advance Access published April 2, 2014. doi:10.1093/sysbio/syu023
+'''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.''' ([http://epubs.siam.org/doi/abs/10.1137/110845045 Abstract])

@@ Line 11: / Line 11: @@
 === Downloads ===
-* [[Media:rspr_1_2_2_source.zip|rspr v1.2.2 source code]]
+* [[Media:rspr_1_3_0_source.zip|rspr v1.3.0 source code]]
 * [[Media:rspr_1_2_1_source.zip|rspr v1.2.1 source code]]
 * [[Media:rspr_1_2_0_source.zip|rspr v1.2.0 source code]]

@@ Line 7: / Line 7: @@
 === Documentation ===
-* [[SPR Supertrees README|README]]
+* [[rSPR README|README]]
 * [[rSPR version history|Version history]]

@@ Line 7: / Line 7: @@
 === Documentation ===
-* [[Media:README_RSPR.txt|README]]
+* [[SPR Supertrees README|README]]
 * [[rSPR version history|Version history]]

@@ Line 31: / Line 31: @@
 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''. 2013.''' (In Preparation).
+'''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''. 2013.''' (In Preparation). ([http://arxiv.org/abs/1305.0512 Preprint])
+'''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])
-'''Whidden, C., Zeh, N., Beiko, R.G. ''Supertrees based on the subtree prune-and-regraft distance''. 2013.''' (Submitted).  ([https://peerj.com/preprints/18/ Preprint])
+'''Whidden, C., Zeh, N., Beiko, R.G. ''Supertrees based on the subtree prune-and-regraft distance''. 2014. Systematic Biology.''' Advance Access published April 2, 2014. 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.''' ([http://epubs.siam.org/doi/abs/10.1137/110845045 Abstract])

@@ Line 1: / Line 1: @@
 __NOTOC__
-rSPR is a software package for calculating rooted subtree-prune-and-regraft distances and rooted agreement forests. Version 1.0.2 includes an implementation of the cluster reduction and is significantly faster than the previous versions in many cases.
+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.
@@ Line 29: / Line 29: @@
 If you use rSPR in your research, please cite:
-'''Whidden, C., Zeh, N., Beiko, R.G. ''Subtree Prune-and-Regraft Supertrees''. 2011.''' (In Preparation).
+'''Whidden, C., Zeh, N., Beiko, R.G.  ''Computing the SPR Distance of Binary Rooted Trees in O(2^k n) Time''. 2013.''' (In Preparation).
 '''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])