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Reconstruction of large phylogenetic trees: A parallel approach

Zhihua Du, Feng Lin, Usman W. Roshan
2005 Computational biology and chemistry  
Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem.  ...  As a case study, our parallel approach only takes 22.1 hours on four processors to outperform the best score to date (found at 123.7 hours by the sequential Rec-I-DCM3 program ) on one dataset.  ...  It provides a fast and practicable approach for parallel inference of large phylogenetic trees containing up to 10,000 sequences.  ... 
doi:10.1016/j.compbiolchem.2005.06.003 pmid:16040277 fatcat:mi2aej3uu5dpfdv5zjw57mgd5y

High-resolution and Deep Phylogenetic Reconstruction of Ancestral States from Large Transcriptomic Data Sets

Sumanth Mutte, Dolf Weijers
2020 Bio-protocol  
Building meaningful phylogenetic trees is needed for the accurate reconstruction of the past.  ...  To achieve a correct phylogenetic understanding of genes or proteins, reliable and robust methods are needed to construct meaningful trees.  ...  Efforts of all the authors are highly appreciated, who developed many extremely useful and efficient programs and algorithms for phylogenetics, and making them freely accessible to the scientific community  ... 
doi:10.21769/bioprotoc.3566 pmid:33659537 pmcid:PMC7842344 fatcat:jp22rmvvgnaivptxpshngyncwe

Implementing Large Genomic SNP Datasets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 Systematic Biology  
We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation.  ...  Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power.  ...  Our SNPs2CF() function can be run in multiple cores in parallel, making it highly efficient with large genomic data sets.  ... 
doi:10.1093/sysbio/syaa005 pmid:32011713 fatcat:4facam7jivao5gj7js32kpjh2q

ClusPhylo: Spark Based Fast and Reliable Approach for Reconstruction of Phylogenetic Network Using Large Databases

S. Malik, S. Khatri, D. Sharma
2017 Journal of Biology and Today s World  
A parallel approach of phylogenetic investigation is built utilizing processing powers that requires top of the line machines.  ...  Currently algorithms for reconstructing phylogenetics are in view of single process model or parallel models (7, 8) , but they cannot scale well with the drastically expanding size of info dataset.  ...  CONFLICT OF INTEREST The authors declared no potential conflicts of interests with respect to the authorship and/or publication of this paper.  ... 
doi:10.15412/j.jbtw.01060602 fatcat:l2qrccqgpjes3ihatdtqebfdwm

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

Hiroki Goto, Oliver A. Ryder, Allison R. Fisher, Bryant Schultz, Sergei L. Kosakovsky Pond, Anton Nekrutenko, Kateryna D. Makova
2011 Genome Biology and Evolution  
Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117-0.186 Ma, significantly preceding  ...  In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial  ...  Additional funding is provided, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.  ... 
doi:10.1093/gbe/evr067 pmid:21803766 pmcid:PMC3194890 fatcat:ob3f3x2f2vdzvfbuwpvm55aqoi

Trees within trees: phylogeny and historical associations

Roderic D.M. Page, Michael A. Charleston
1998 Trends in Ecology & Evolution  
dynamic programming approach.  ...  Parallels among these problems raise the tantalizing prospect that each is a special case of a more general problem, and that a single analytical tool can be applied to all three kinds of association.  ... 
doi:10.1016/s0169-5347(98)01438-4 pmid:21238340 fatcat:7dz27dvnsjc6pbssyudtbtodzi

The inference of gene trees with species trees [article]

Gergely J. Szöllosi, Eric Tannier, Vincent Daubin, Bastien Boussau
2013 arXiv   pre-print
Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa.  ...  In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences.  ...  This computational difficulty is a major hurdle to using this approach on large data sets, containing large numbers of species, and large numbers of gene families.  ... 
arXiv:1311.0651v1 fatcat:nwhpj4yuojcwdinu5jcxjhsiie

Maximum gene-support tree

Yunfeng Shan, Xiu-Qing Li
2008 Evolutionary Bioinformatics  
Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the "true tree" by all the four algorithms.  ...  Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available.  ...  The authors greatly appreciate helpful suggestions and comments of the two reviewers.  ... 
pmid:19204816 pmcid:PMC2614190 fatcat:l4ln42rj4rg7dj3wf7ef6vk3em

A work stealing based approach for enabling scalable optimal sequence homology detection

Jeff Daily, Ananth Kalyanaraman, Sriram Krishnamoorthy, Abhinav Vishnu
2015 Journal of Parallel and Distributed Computing  
. • First implementation of suffix tree construction using distributed work stealing. • Evaluation of many dynamic load balancing strategies for optimal homology detection. • Parallel efficiency of 75%  ...  Results for 2.56 M sequences on up to 8K cores show parallel efficiencies of ∼75%-100%, a time-to-solution of 33 s, and a rate of ∼2.0 M alignments per second.  ...  Acknowledgments This work was supported in parts by the DOE Office of  ... 
doi:10.1016/j.jpdc.2014.08.009 fatcat:nqlqskbv2rginpfg2act4rskke

The Inference of Gene Trees with Species Trees

Gergely J. Szöllősi, Eric Tannier, Vincent Daubin, Bastien Boussau
2014 Systematic Biology  
Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa.  ...  In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences.  ...  A/1-11-1-2012-0001 "National Excellence Program."  ... 
doi:10.1093/sysbio/syu048 pmid:25070970 pmcid:PMC4265139 fatcat:lsfkomvpfzdkff6gec46y34d6a

Computing phylogenetic trees using topologically related minimum spanning trees

Prabhav Kalaghatgi, Thomas Lengauer
2017 Journal of Graph Algorithms and Applications  
The indeterminacy of CLGrouping can be removed if the input MST shares a topological relationship with the corresponding phylogenetic tree.  ...  inferring phylogenetic trees.  ...  We thank the reviewers for their constructive criticism of the first version of the manuscript.  ... 
doi:10.7155/jgaa.00447 fatcat:yet3g7qdknephekel3tdg7tyym

Parallel computation of phylogenetic consensus trees

Andre J. Aberer, Nicholas D. Pattengale, Alexandros Stamatakis
2010 Procedia Computer Science  
In this paper we focus on a post-analysis task in reconstructing very large trees, specifically the step of building (extended) majority rules consensus trees from a collection of equally plausible trees  ...  In the field of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is becoming an increasingly important issue for operations other than the tree reconstruction  ...  a performance bottleneck for reconstructing very large trees in terms of number of taxa.  ... 
doi:10.1016/j.procs.2010.04.118 fatcat:7qw3jrs6yvavbizpmhp4cdei6y

Gene Trees in Species Trees

Wayne P. Maddison, John J. Wiens
1997 Systematic Biology  
Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud  ...  Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes  ...  me not to be too sure about phylogeny as a history of realized genetic descent, and David Cannatella for suggesting the term "cloudogram" for Figure 9 (which I was, alas, too reserved to use).  ... 
doi:10.1093/sysbio/46.3.523 fatcat:ltvovs4qlfes3ozxj2bhx7mwpa

Gene Trees in Species Trees

Wayne P. Maddison
1997 Systematic Biology  
Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud  ...  Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes  ...  me not to be too sure about phylogeny as a history of realized genetic descent, and David Cannatella for suggesting the term "cloudogram" for Figure 9 (which I was, alas, too reserved to use).  ... 
doi:10.2307/2413694 fatcat:zzd6nn6lsrg6ldei6qqw7j7nka

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, Manolis Kellis
2012 Systematic Biology  
Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications.  ...  tree reconstructions.  ...  We believe this is a result of large species trees generating large gene trees so that many branches in the gene tree reconstruction are uncertain.  ... 
doi:10.1093/sysbio/sys076 pmid:22949484 pmcid:PMC3526801 fatcat:xqvew4y4erfibcudaccdfj6vdi
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