Rogue (Q60638): Difference between revisions

← Older edit

@@ Property / last update @@
-March 2023Timestamp +2023-03-20T00:00:00Z
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-R
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-ape
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-Normal rank
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-cli
@@ Property / imports: cli / rank @@
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-fastmatch
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-grDevices
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-matrixStats
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-Rdpack
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-utils
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@@ Property / cites work @@
-Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
-Normal rank
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-Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
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@@ Property / software version identifier @@
+.0.0
@@ Property / software version identifier: 1.0.0 / rank @@
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+publication date: 13 September 2021Timestamp +2021-09-13T00:00:00Z
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@@ Property / last update: 29 November 2023 / rank @@
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@@ Property / description @@
+Rogue ("wildcard") taxa are leaves with uncertain phylogenetic  position.  Their position may vary from tree to tree under inference methods that yield a  tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).  The presence of rogue taxa in a tree set can potentially remove all  information from a consensus tree. The information content of a consensus  tree - a function of its resolution and branch support values - can often be  increased by removing rogue taxa.   'Rogue' provides an explicitly information-theoretic approach to rogue  detection (Smith 2022) <doi:10.1093/sysbio/syab099>,  and an interface to 'RogueNaRok' (Aberer et al. 2013)  <doi:10.1093/sysbio/sys078>.
+Normal rank
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+Martin R. Smith
@@ Property / author: Martin R. Smith / rank @@
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+Andre J. Aberer
@@ Property / author: Andre J. Aberer / rank @@
+Normal rank
@@ Property / copyright license @@
+GNU General Public License
@@ Property / copyright license: GNU General Public License / rank @@
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@@ Property / copyright license: GNU General Public License / qualifier @@
+edition/version: ≥ 3 (English)
@@ Property / imports @@
+ape
@@ Property / imports: ape / rank @@
+Normal rank
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+software version identifier: ≥ 5.0
@@ Property / imports @@
+cli
@@ Property / imports: cli / rank @@
+Normal rank
@@ Property / imports: cli / qualifier @@
+software version identifier: ≥ 3.0
@@ Property / imports @@
+fastmatch
@@ Property / imports: fastmatch / rank @@
+Normal rank
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+grDevices
@@ Property / imports: grDevices / rank @@
+Normal rank
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+matrixStats
@@ Property / imports: matrixStats / rank @@
+Normal rank
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+Rdpack
@@ Property / imports: Rdpack / rank @@
+Normal rank
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+software version identifier: ≥ 0.7
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+Rfast
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+stats
@@ Property / imports: stats / rank @@
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+TreeDist
@@ Property / imports: TreeDist / rank @@
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+software version identifier: > 2.2.0
@@ Property / imports @@
+TreeTools
@@ Property / imports: TreeTools / rank @@
+Normal rank
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+software version identifier: ≥ 1.9.1.9003
@@ Property / imports @@
+utils
@@ Property / imports: utils / rank @@
+Normal rank
@@ Property / cites work @@
+Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
+Normal rank
@@ Property / cites work @@
+Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
+Normal rank
@@ Property / depends on software @@
+R
@@ Property / depends on software: R / rank @@
+Normal rank
@@ Property / depends on software: R / qualifier @@
+software version identifier: ≥ 3.5.0
@@ Property / MaRDI profile type @@
+MaRDI software profile
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+Normal rank
@@ links / mardi / name / links / mardi / name @@
+Software:60638

Latest revision as of 19:56, 12 March 2024

Identify Rogue Taxa in Sets of Phylogenetic Trees

Language	Label	Description	Also known as
English	Rogue	Identify Rogue Taxa in Sets of Phylogenetic Trees

Statements

software version identifier

2.1.5

publication date

20 March 2023

0 references

1.0.0

publication date

1 July 2021

0 references

2.0.0

publication date

13 September 2021

0 references

2.1.0

publication date

13 January 2022

0 references

2.1.1

publication date

20 July 2022

0 references

2.1.2

publication date

16 August 2022

0 references

2.1.3

publication date

26 September 2022

0 references

2.1.4

publication date

16 January 2023

0 references

2.1.6

publication date

29 November 2023

0 references

0 references

0 references

0 references

0 references

29 November 2023

0 references

description

Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.

0 references

0 references

0 references

GNU General Public License

edition/version

≥ 3 (English)

0 references

imports