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Inference of Large Phylogenies Using Neighbour-Joining [chapter]

Martin Simonsen, Thomas Mailund, Christian N. S. Pedersen
2011 Communications in Computer and Information Science  
Inference of such large phylogenies takes hours or days using the Neighbour-Joining method on a normal desktop computer because of the O(n 3 ) running time.  ...  RapidNJ is a search heuristic which reduce the running time of the Neighbour-Joining method significantly but at the cost of an increased memory consumption making inference of large phylogenies infeasible  ...  Introduction The neighbour-joining (NJ) method [10] is a widely used method for phylogenetic inference, made popular by reasonable accuracy combined with a cubic running time algorithm by Studier and  ... 
doi:10.1007/978-3-642-18472-7_26 fatcat:etrrowz5wrhyldpmktpijjo7pm

Towards a practical O(nlogn) phylogeny algorithm

Jakub Truszkowski, Yanqi Hao, Daniel G Brown
2012 Algorithms for Molecular Biology  
An early prototype implementation of our software is available at Any useful phylogenetic reconstruction algorithm must use (n log n) time to reconstruct a phylogeny of n taxa, because it takes that much  ...  We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of Neighbour Joining , which requires (n 3 ) runtime  ...  award to YH; from the Province of Ontario through an Early Researcher Award to DGB; and from a Cheriton Scholarship to JT.  ... 
doi:10.1186/1748-7188-7-32 pmid:23181935 pmcid:PMC3561654 fatcat:4gqpmnmcjrhsxdwuxtlw7ammqa

Towards a Practical O(n logn) Phylogeny Algorithm [chapter]

Daniel G. Brown, Jakub Truszkowski
2011 Lecture Notes in Computer Science  
An early prototype implementation of our software is available at Any useful phylogenetic reconstruction algorithm must use (n log n) time to reconstruct a phylogeny of n taxa, because it takes that much  ...  We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of Neighbour Joining , which requires (n 3 ) runtime  ...  award to YH; from the Province of Ontario through an Early Researcher Award to DGB; and from a Cheriton Scholarship to JT.  ... 
doi:10.1007/978-3-642-23038-7_2 fatcat:sk4axi4n7zai5dlthqrzhzqq3m

Improving phylogenetic inference from morphology: data from modern Crocodylia

Roland B Sookias
2019 Zenodo  
Poster presented at Society of Vertebrate Paleontology Annual General Meeting, Albuquerque 2018  ...  neighbour joining tree based on distance matrix of 3D surface scans of crania using Procrustes superposition of surfaces using the method from [4] .  ...  Phylogenies inferred using molecular and morphological data often disagree for modern taxa.  ... 
doi:10.5281/zenodo.2566465 fatcat:oqj7p7qwurag5p2ya77vhzla6m

The evolution of tumour phylogenetics: principles and practice

Russell Schwartz, Alejandro A. Schäffer
2017 Nature reviews genetics  
Acknowledgements This research was supported in part by the Intramural Research Program of the National Library of Medicine (part of the US National Institutes of Health) and by a grant from the Pennsylvania  ...  Department of Health (grant number 4100070287).  ...  joining 56 Regional aCGH Neighbour joining 145 scSeq-based CNVs Neighbour joining 71 ‡ WGA scSeq Neighbour joining 156 scSeq Neighbour joining 80 scSeq Neighbour joining 185 CNVs  ... 
doi:10.1038/nrg.2016.170 pmid:28190876 pmcid:PMC5886015 fatcat:h2rpqbaxdjfkxdbaj7nlirw6xy

Fast phylogenetic DNA barcoding

K. Munch, W. Boomsma, E. Willerslev, R. Nielsen
2008 Philosophical Transactions of the Royal Society of London. Biological Sciences  
We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping.  ...  We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment  ...  using bootstrapped neighbour joining.  ... 
doi:10.1098/rstb.2008.0169 pmid:18852104 pmcid:PMC2607413 fatcat:dyfvkrziaffc3pczxeo5lb5yaq

Molecular phylogeny applied to species and related ascomycetous yeasts

T BOEKHOUT
2004 FEMS Yeast Research  
The alignments of the three genes and of deduced amino acid sequences of the actin gene were used in phylogenetic analyses by parsimony and neighbour-joining methods as single and combined datasets.  ...  Phylogenetic relationships inferred by actin and SSU gene sequences agreed to a large extent.  ... 
doi:10.1016/j.femsyr.2003.12.001 fatcat:t5yr7256vfgarchqydqrox5ewu

Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage

J. F. Saldarriaga
2003 International Journal of Systematic and Evolutionary Microbiology  
suggested in previous SSU rRNA and actin phylogenies.  ...  all three proteincoding genes, and phylogenetic trees were inferred.  ...  (in the large weighted neighbour-joining tree, Fig. 4 , it also branches at the base of dinoflagellates, but as sister to a ciliate, Stylonychia).  ... 
doi:10.1099/ijs.0.02328-0 pmid:12656195 fatcat:wvlkx2q6xjelbag2s3ein6bvvm

Molecular phylogenetics of sexual and parthenogenetic Timema walking-sticks

C. Sandoval, D. A. Carmean, B. J. Crespi
1998 Proceedings of the Royal Society of London. Biological Sciences  
We inferred a phylogeny for the walking-stick genusTimema (Insecta: Phasmatoptera) using mitochondrial DNA sequence, and we used the phylogeny to infer temporal patterns of speciation and the evolutionary  ...  Maximum parsimony, neighbour-joining and maximum-likelihood analyses of 660 base pairs (bp) of cytochrome oxidase I (COI) yielded phylogenies that were well resolved and topologically identical or very  ...  In this paper, we infer a phylogeny for all 13 described species of Timema using mitochondrial DNA (mtDNA) sequence.  ... 
doi:10.1098/rspb.1998.0335 pmcid:PMC1689018 fatcat:gdb32v2bzbhqxn72fsqiytifii

Complete mitochondrial genome of Pelecanus crispus and its phylogeny

Tian Huang, Yonghong Wang, Libo Zhou, Zhenggang Xu
2019 Mitochondrial DNA Part B: Resources  
This information will be useful in the current understanding of the phylogeny and evolution of Pelecaniformes.  ...  It is a large waterfowl that is of international concern. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of P. crispus.  ...  Phylogenetic tree of the relationships among Pelecaniformes and its related orders were presented using complete mitochondrial genome among 26 pelecaniformes species using neighbour-joining analyses in  ... 
doi:10.1080/23802359.2019.1666679 pmid:33365862 pmcid:PMC7706529 fatcat:2lalh67pnrh77kcyhqetihiuam

Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies [chapter]

Yunfeng Shan, Robin Gras
2010 Advances in Experimental Medicine and Biology  
36 single genes of six plants inferred 18 unique trees using maximum parsimony.  ...  For inferring the congruent tree, the minimum 30 genes were required. This approach may provide potential power in resolving conflictions of phylogenies.  ...  Roy for setting up this research before he left Department of Biology, Life Sciences Centre, Dalhousie University and discussed a couple of preliminary algorithms.  ... 
doi:10.1007/978-1-4419-5913-3_27 pmid:20865506 fatcat:qiarma6bfje5rgzagxhyp77trm

Fast reconstruction of phylogenetic trees using locality-sensitive hashing [article]

Daniel G. Brown, Jakub Truszkowski
2012 arXiv   pre-print
Via a prototype and a sequence of large-scale experiments, we show that many large phylogenies can be reconstructed fast, without compromising reconstruction accuracy.  ...  For phylogenies with very short branches, the running time of our algorithm is close to linear.  ...  This theoretical algorithm shows the possibility of reconstructing such large phylogenies in sub-quadratic time from short sequences, without compromising the accuracy.  ... 
arXiv:1111.0379v2 fatcat:3jufuol2ynghjeqxeli2l37r24

Phylogenetic relationships of three hymenolepidid species inferred from nuclear ribosomal and mitochondrial DNA sequences

M. OKAMOTO, T. AGATSUMA, T. KUROSAWA, A. ITO
1997 Parasitology  
 Three hymenolepidid tapeworms, Hymenolepis diminuta, H. nana and H. microstoma, are commonly maintained in laboratory rodents and used in many experimental model systems of tapeworm infections.  ...  We examined partial sequences from the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences to infer phylogenetic relationships of  ...  Phylogenetic trees inferred from different sequences were also very similar, except for genetic distances. Furthermore, bootstrap values of the node in neighbour-joining trees were large.  ... 
doi:10.1017/s0031182097001741 pmid:9488878 fatcat:toohbi7lpjfy5glnmsm4tq5lu4

GeneSupport Maximum Gene-Support Tree Approach to Species Phylogeny Inference [article]

Yunfeng Shan, Xiu-Qing Li
2009 arXiv   pre-print
It is suitable for phylogenetic methods such as maximum parsimony, maximum likelihood, Baysian and neighbour-joining, which is used to reconstruct single gene trees firstly with a variety of phylogenetic  ...  inference programs.  ...  Felsenstein for permit the use of his publicly available code from the program treedist of PHYLIP package.  ... 
arXiv:0910.1953v1 fatcat:kkv6u54cgnahljd6hbahhd5rfa

TCS: a computer program to estimate gene genealogies

M. Clement, D. Posada, K. A. Crandall
2000 Molecular Ecology  
Sloan Foundation, a Shannon Award from the National Institutes of Health, and NIH R01-HD34350.  ...  These traditional methods such as parsimony, neighbour-joining, and maximumlikelihood make assumptions that are invalid at the population level.  ...  Yet phylogenies are only as useful as they are accurate.  ... 
doi:10.1046/j.1365-294x.2000.01020.x pmid:11050560 fatcat:7xabecmvpvbz5i7gt5tnyk4gj4
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