Filters








156,262 Hits in 3.4 sec

Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees [article]

Wai-Tong Louis Fan, Sebastien Roch
2019 arXiv   pre-print
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

Uyen Mai, Erfan Sayyari, Siavash Mirarab, Gabriel Moreno-Hagelsieb
2017 PLoS ONE  
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

Howard A Ross, David C Nickle, Yi Liu, Laura Heath, Mark A Jensen, Allen G Rodrigo, James I Mullins
2007 Evolutionary Bioinformatics  
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

Taylor Wade, L. Thiberio Rangel, Soumya Kundu, Gregory P. Fournier, Mukul S. Bansal, Marc Robinson-Rechavi
2020 PLoS ONE  
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

Jialiang Yang, Jun Li, Liuhuan Dong, Stefan Grunewald
2011 BMC Bioinformatics  
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

Guoliang Li, Mike Steel, Louxin Zhang, Todd Oakley
2008 Systematic Biology  
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

Xingyu Yang, Christopher M Tipton, Matthew C Woodruff, Enlu Zhou, F Eun-Hyung Lee, Inãki Sanz, Peng Qiu
2020 BMC Genomics  
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]

G. L. Li, M. Steel, L. X. Zhang
2008 arXiv   pre-print
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]

Xingyu Yang, Christopher M. Tipton, Matthew C. Woodruff, Enlu Zhou, F. Eun-Hyung Lee, Inãki Sanz, Peng Qiu
2018 bioRxiv   pre-print
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]

Mareike Fischer, Bhalchandra D. Thatte
2009 arXiv   pre-print
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

Gregory B Ewing, Ingo Ebersberger, Heiko A Schmidt, Arndt von Haeseler
2008 BMC Evolutionary Biology  
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

Tony W. Lai, Derick Wood
1994 RAIRO - Theoretical Informatics and Applications  
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)

Karel Šilhán
2018 Geografie-Sbornik CGS  
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]

Jianming Huang, Yu Hua
2021 arXiv   pre-print
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?

Armin Hoenen, Steffen Eger, Ralf Gehrke
2017 Proceedings of the 15th Meeting on the Mathematics of Language  
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
« Previous Showing results 1 — 15 out of 156,262 results