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Discriminative Measures for Comparison of Phylogenetic Trees [article]

Omur Arslan, Dan P. Guralnik, Daniel E. Koditschek
2015 arXiv   pre-print
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees.  ...  A relaxation of this formula to a simple count yields another measure on all trees --- the crossing dissimilarity d_CM.  ...  Acknowledgements This work was funded in part by the Air Force Office of Science Research under the MURI FA9550-10-1-0567. Appendix A. Proofs  ... 
arXiv:1310.5202v2 fatcat:octqpbw2tzfjbo4idxdxeigyfm

Discriminative measures for comparison of phylogenetic trees

Omur Arslan, Dan P. Guralnik, Daniel E. Koditschek
2017 Discrete Applied Mathematics  
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees.  ...  Abstract In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees.  ...  Acknowledgements This work was funded in part by the Air Force Office of Science Research under the MURI FA9550-10-1-0567. Appendix A. Proofs  ... 
doi:10.1016/j.dam.2016.10.003 fatcat:f5craz7ha5hdxaefd7rw4kf2am

MASTtreedist: Visualization of Tree Space Based on Maximum Agreement Subtree

Hong Huang, Yongji Li
2013 Journal of Computational Biology  
Such a new phylogenetic tree comparison metric improves the visualization of taxa differences by discriminating small divergences of subtree structures for phylogenetic tree reconstruction.  ...  This new comparison module provides a new treetree pairwise comparison metric based on the differences of the number of MAST leaves among constructed phylogenetic trees.  ...  Acknowledgements The authors would like to express their gratitude to David Swofford, and James Wilgenbusch for insightful suggestions, and comments on this research.  ... 
doi:10.1089/cmb.2012.0243 pmid:23294272 fatcat:jzdlp3horrc45pm4463whym2t4

Nonmetric Distances for Barcode of Life

Hisamitsu Akiba, Y-h. Taguchi
2008 IPSJ Transactions on Bioinformatics  
The nonmetric multidimensional scaling method enables to discriminate higher taxa compared to tree construction by the neighbor-joining method or the maximum parsimony method with raw distance measure,  ...  For example, the ratio of mean inner taxa nonmetric distance to the intertaxa distance is smaller than that for raw (metric) distance.  ...  Each family is numbered for comparison with the phylogenetic tree (Fig. 5) . Number in bold is TP for each family. minimized.  ... 
doi:10.2197/ipsjtbio.1.35 fatcat:53m3uuee2zcrldeunjhmszbxky

Interactive visual comparison of multiple trees

Sebastian Bremm, Tatiana von Landesberger, Martin Hess, Tobias Schreck, Philipp Weil, Kay Hamacherk
2011 2011 IEEE Conference on Visual Analytics Science and Technology (VAST)  
A new tree comparison score has been elaborated for the identification of interesting patterns.  ...  Typically, the analysis considers multiple phylogenetic trees, either to account for statistical significance or for differences in derivation of such evolutionary hierarchies; for example, based on different  ...  ACKNOWLEDGEMENTS We are grateful to the Fonds der chemischen Industrie for their financial support.  ... 
doi:10.1109/vast.2011.6102439 dblp:conf/ieeevast/BremmLHSWH11 fatcat:inlvjnjifbd5rapceqhxl6quga

Is body shape of varanid lizards linked with retreat choice?

Graham G. Thompson, Christofer J. Clemente, Philip C. Withers, Bryan G. Fry, Janette A. Norman
2008 Australian journal of zoology (Print)  
dug into the ground, those that retreat to spaces under rocks or in tree hollows, and those that retreat to trees but not tree hollows) accounted for much of the variation in body shape.  ...  In our earlier analysis of Varanus body shape, size was a dominating factor with some qualitative phylogenetic patterns and grouping of species into ecological categories.  ...  A comparison of the discriminating power among the species used in both size-free, and size-free and phylogenetically corrected analysis was undertaken by comparing Wilks' lambda scores.  ... 
doi:10.1071/zo08030 fatcat:2b225dasobffxevp3xw5j6uqdy

New method for comparing DNA primary sequences based on a discrimination measure

Jie Feng, Yong Hu, Ping Wan, Aibing Zhang, Weizhong Zhao
2010 Journal of Theoretical Biology  
Using the primitive discrimination substrings of sequence S and Q, a discrimination measure DM(S, Q) is defined for the similarity analysis of them.  ...  The core of our method is a new measure of pairwise distances among sequences.  ...  Acknowledgements We thank all the anonymous referees for their valuable suggestions and support.  ... 
doi:10.1016/j.jtbi.2010.07.040 pmid:20688082 pmcid:PMC7094107 fatcat:v2uo77yrcjff7pwkq53qgocuvy

Clustering Organisms Using Metabolic Networks [chapter]

Tomasz Arodź
2008 Lecture Notes in Computer Science  
Finally, we show that the phylogenetic tree constructed using network-based approach agrees in most cases with gene-based phylogeny.  ...  Topological properties of metabolic networks may reflect systematic differences between evolutionary distinct groups of organisms.  ...  For comparison, if the same supervised LDA method is applied to our vertexspecific descriptors based on vertex degrees, as shown in the left panel of Fig. 3 , discrimination between groups of organisms  ... 
doi:10.1007/978-3-540-69387-1_60 fatcat:kxmwxxuvubad7myy24xowz26x4

Algorithms for Computing Cluster Dissimilarity between Rooted Phylogenetic Trees

Li Shuguang, Liu Zhihui
2015 Open Cybernetics and Systemics Journal  
One way of mining phylogenetic information databases would be to compare the trees by using a tree comparison measure.  ...  Presented here are a new dissimilarity measure for comparing rooted trees and three algorithms to efficiently compute it.  ...  Tree comparison concerns three related problems: to construct a consensus tree for a given set of trees [17] , to compute a consensus index for a given set of trees [18, 19] , and to measure pairwise  ... 
doi:10.2174/1874110x01509012218 fatcat:skuhz2obkvaldnkiujv3pitadm

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

Jia-Ming Chang, Paolo Di Tommaso, Cedric Notredame
2014 Molecular biology and evolution  
We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set.  ...  We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees.  ...  Acknowledgments The authors thank Eyal Privman for helping benchmark HoT and GUIDANCE, and Jose Castresana and Salvador Capella for providing the data necessary for the phylogenetic validation benchmark  ... 
doi:10.1093/molbev/msu117 pmid:24694831 fatcat:dgxofl4lbrchnngv5h5qw6uxzy

Inferring Tumour Proliferative Organisation from Phylogenetic Tree Measures in a Computational Model [article]

Jacob G Scott, Alexander RA Anderson, Philip K Maini, Alexander G Fletcher
2018 bioRxiv   pre-print
Given the advent of multi-region sampling, and the opportunities offered by them to understand tumour evolutionary history, we focus on a suite of statistical measures of the phylogenetic trees resulting  ...  We find strikingly different patterns in these measures for changing symmetric division probability which hinge on the inclusion of spatial constraints.  ...  AGF is supported by a Vice-Chancellor's Fellowship from the University of Sheffield.  ... 
doi:10.1101/334946 fatcat:xc6w737wcfgy3bevqwwj2r7yse

THE POTENCY OF ANGLE MEASUREMENT AND COMPARISON OF VEIN LENGTHS IN DISTINGUISHING BACTROCERA SPECIES COMPLEXES

Gesang Pratyadhiraksana, Tri Murniningtyas Puji Lestari, Rudi Hari Murti, Suputa Suputa
2020 Jurnal Hama dan Penyakit Tumbuhan Tropika  
The potency of angle measurement and comparison of vein lengths in distinguishing Bactrocera species complexes.  ...  One of the most conspicuous features of Bactrocera fruit flies is their wing, which can be elaborated for identification.  ...  ACKNOWLEDGMENTS The authors would like to thank the staffs from Sorong Quarantine, Laboratory of Vapor Heat Treatment BBPOPT, and Laboratory of Basic Entomology, Universitas Gadjah Mada for providing the  ... 
doi:10.23960/j.hptt.22092-99 fatcat:4tjdm77m5bam5gitijbzp2yxdq

Page 131 of The Journal of Ecology Vol. 102, Issue 1 [page]

2014 The Journal of Ecology  
PHYLOGENETIC SIGNAL FOR FLORAL COLOUR The two measures of phylogenetic signal, A and K, have different interpretations, but the results are compatible and suggest that floral colours in related species  ...  Results of phylogenetic anova for MAD and minAD metrics (fit between chromatic cues and hymenopteran hue discrimination).  ... 

Morphometric discrimination of females of five species of Anopheles of the subgenus Nyssorhynchus from Southern and Northwest Colombia

David A Calle L, Martha L Quiñones, Holmes F Erazo, Nicolás Jaramillo O
2002 Memórias do Instituto Oswaldo Cruz  
on the tree represent equal evolutionary distances for each species; however our comparison only seeks to establish concordance between the phenetic similarities of the species and their phylogenetic  ...  Mahalanobis distances were used for the discriminant analysis, these being a measure of the distance of each individual from the centroid of each species.  ... 
doi:10.1590/s0074-02762002000800021 fatcat:cgqdpfv3ircxfctc7dxfmrggym

Phylogenetic Properties of RNA Viruses

Simone Pompei, Vittorio Loreto, Francesca Tria, Yamir Moreno
2012 PLoS ONE  
A new word, phylodynamics, was coined to emphasize the interconnection between phylogenetic properties, as observed for instance in a phylogenetic tree, and the epidemic dynamics of viruses, where selection  ...  In our work, we reconstruct and analyze the phylogenetic trees of six RNA viruses, with a special emphasis on the human Influenza A virus, due to its relevance for vaccine preparation as well as for the  ...  From all said above, we expect that suitable imbalance measures performed on the Influenza A virus should reveal a high level of imbalance of the corresponding phylogenetic tree.  ... 
doi:10.1371/journal.pone.0044849 pmid:23028645 pmcid:PMC3447819 fatcat:alicflzhrjdhhc2dxvxjixy5om
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