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Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
[article]
2019
arXiv
pre-print
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We establish necessary and sufficient conditions for consistent root reconstruction in continuous-time Markov models with countable state space on bounded-height trees. ...
We also derive quantitative bounds on the error of reconstruction. ...
Root reconstruction In the root reconstruction problem we seek a good estimator of the root state X ρ based on the leaf states X ∂T . ...
arXiv:1707.05702v3
fatcat:dgzjjjr7xja7jlzvxla7wi5qhe
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
2017
PLoS ONE
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Any tree has at least one local MV. Proposition 3. The global MV of any tree is one of its local MVs. Proposition 4. Let p denote the global MV of T . ...
When the global MV is on one of the adjacent edges of r, let a random variable X indicate the distance of the global MV to the root; then, E(X) = 0. d i (p) (S3) ...
A An example tree T rooted at r with a point p on edge (u, v).
Lemma 3 . 3 Consider an edge e = (u, v) of tree T . ...
doi:10.1371/journal.pone.0182238
pmid:28800608
pmcid:PMC5553649
fatcat:qjxz5njwmreupioxgxiajno2vy
Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes
2007
Evolutionary Bioinformatics
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the ancestor on that tree, from (d) the sequence format, and from (e) the number of input sequences. ...
We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c) reconstructing ...
the root node on the tree, and the direct infl uence of the outgroup sequence on the reconstruction of character states at interior nodes in the tree. ...
pmid:19455202
pmcid:PMC2674662
fatcat:czxrqvz25zbq7kwsoxzjhyk5dm
Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families
2020
PLoS ONE
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methods based on branch-lengths are generally robust to gene tree reconstruction error. ...
Our simulation study is based on 6000 true and reconstructed gene trees on 100 species and characterizes the rooting accuracy of the four methods under 36 different evolutionary conditions and 3 levels ...
methods based on branch-lengths are generally robust to gene tree reconstruction error. ...
doi:10.1371/journal.pone.0232950
pmid:32413061
fatcat:o2jga2k45nbfzoygyyxbnsafsa
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states
2011
BMC Bioinformatics
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The reconstruction accuracies on 1000 simulated Yule trees also exhibit similar behaviors. ...
As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their ...
Reconstruction Accuracies on Comb-shaped Trees Due to their extreme unbalanceness, comb-shaped trees (or rooted caterpillars) are widely studied. ...
doi:10.1186/1471-2105-12-18
pmid:21501472
pmcid:PMC3101186
fatcat:2uvyzuy5frcfll5jrpytdafv5y
More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States
2008
Systematic Biology
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state reconstruction. ...
ACKNOWLEDGMENTS The authors thank the anonymous reviewers and Todd Oakley for pointing out related references and helpful comments on the relevance of the results to applying the fossil records to ancestral ...
support for the accuracy of root state reconstruction using a single species to be higher on real trees. ...
doi:10.1080/10635150802203898
pmid:18709600
fatcat:oepod636hzblpd3diuj47shpru
GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data
2020
BMC Genomics
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Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. ...
GLaMST outperforms state-of-art in reconstruction of the BCR lineage tree in both efficiency and accuracy. ...
There may exist one or several one-base operations that can take the root sequence one step closer to all those four nodes. ...
doi:10.1186/s12864-020-06936-w
pmid:32900378
pmcid:PMC7488003
fatcat:uvvympdzgverlcfo6vlrq6aq2e
More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States
[article]
2008
arXiv
pre-print
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support for the accuracy of root state reconstruction using a single
species to be higher on real trees. ...
Effects of tree shape on the accuracy of maximum likelihood-based
ancestor reconstruction, Syst. Biol. 53:809-814.
Mossel, E. 2001. Reconstruction on trees: Beating the second eigenvalue. ...
arXiv:0803.0195v1
fatcat:ssx7apcrkre6ppfsezcfqcifsq
GLaMST: Grow Lineages along Minimum Spanning Tree for B Cell Receptor Sequencing Data
[article]
2018
bioRxiv
pre-print
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Therefore, reconstructing the lineage tree from experimental data requires algorithms to build the tree based on partially observed tree nodes. ...
We developed a new algorithm named Grow Lineages along Minimum Spanning Tree (GLaMST), which efficiently reconstruct the lineage tree given observed BCR sequences that correspond to a subset of the tree ...
There may exist one or several one-base operations that can take the root sequence one step closer to all those four nodes. ...
doi:10.1101/465476
fatcat:yxufjaiavfhnjb23xi4bfza4qu
Maximum Parsimony on Subsets of Taxa
[article]
2009
arXiv
pre-print
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tree and a character. ...
the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa. ...
The authors also provided an example of a phylogenetic tree for which MP for the reconstruction of the root state works more reliably on a subset of taxa closer to the root than on all taxa. ...
arXiv:0809.3653v2
fatcat:tah2x7x45fairg7ts33xwyta2e
Rooted triple consensus and anomalous gene trees
2008
BMC Evolutionary Biology
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In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. ...
Results: Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. ...
However we also note that if the rooted triplet trees do conflict then the reconstructed tree will depend on the order the taxa are added. ...
doi:10.1186/1471-2148-8-118
pmid:18439266
pmcid:PMC2409437
fatcat:4oozhb3yvrcyplvuirctbdofbq
Updating approximately complete trees
1994
RAIRO - Theoretical Informatics and Applications
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Finally, the cost of reconstructing a subtree rooted on level 0 is O (n), but it is required only when we cannot update a subtree T rooted on level h/3. ...
The cost of reconstructing a subtree rooted on level h/3 is O (n 2 / 3 ), but it is necessary only when we cannot update a subtree rooted on level 2 h/3. ...
doi:10.1051/ita/1994280504311
fatcat:t2prb3ugbbg3tchut3c4wtpwhq
Detailed reconstruction of gully headcut retreat using exposed tree roots: a case study from the Vsetínské vrchy Mts. (Outer Western Carpathians)
2018
Geografie-Sbornik CGS
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This study aims to asses newly originated gully development based on an analysis of exposed tree roots. ...
Dendrogeomorphic (tree ring-based) methods are a good alternative approach for assessing gully development in forested areas. ...
On the other hand, gully erosion has rarely been studied using exposed tree roots. ...
doi:10.37040/geografie2018123020179
fatcat:n7bzr3l5ynfy7jqr2qsabqc7sa
Update the Root of Integrity Tree in Secure Non-Volatile Memory Systems with Low Overhead
[article]
2021
arXiv
pre-print
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Moreover, the SIT root is difficult to be reconstructed from the leaf nodes since updating one tree node needs its parent node as input. ...
In this paper, we propose an efficient and low-latency scheme, called SCUE, to directly update the root on the SGX integrity tree (SIT) by overlooking the updates upon the intermediate tree nodes. ...
., the attacks are detected after reconstructing the whole integrity tree and comparing the reconstructed root with the stored one. ...
arXiv:2103.03502v1
fatcat:qs3wtvj7bzhfhcifcnkyyve3gy
How Many Stemmata with Root Degree k?
2017
Proceedings of the 15th Meeting on the Mathematics of Language
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While Maas' argument was based on one example with a tradition of three surviving manuscripts, we show in this paper that for the whole class of trees corresponding to Maasian reconstructed stemmata and ...
We find that root bifurcations are extremely numerous in both kinds of trees. ...
A rooted Greg tree therefore symbolizes a reconstructed stemma. ...
doi:10.18653/v1/w17-3402
dblp:conf/mol/HoenenEG17
fatcat:56xt7xou7vdphbfocorebozd7u
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