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Fast Algorithms for Inferring Evolutionary Trees

RICHA AGARWALA, DAVID FERNÁNDEZ-BACA, GIORA SLUTZKI
1995 Journal of Computational Biology  
The rst algorithm is faster than a previous algorithm by Gus eld when the input matrix for the problem is sparse. Next, we present t wo online algorithms.  ...  We present algorithms for the perfect phylogeny problem restricted to binary characters.  ...  Introduction A fundamental problem in molecular biology is that of inferring the evolutionary history of a set of species, each of which is speci ed by the set of traits or characters that it exhibits  ... 
doi:10.1089/cmb.1995.2.397 pmid:8521270 fatcat:5myrxxuotzaz3guwdmbuhiejae

A New Fast Method For Inferring Multiple Consensus Trees Using K-Medoids

Nadia Tahiri
2018 Zenodo  
Material and methods We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e  ...  Conclusions The presented method allows for inferring multiple consensus trees from a given set of gene trees.  ... 
doi:10.5281/zenodo.1184232 fatcat:yjhzz36ndfdhxp6o3cb5ro73l4

Applications and Algorithms for Inference of Huge Phylogenetic Trees: a Review

Muhammad Sardaraz, Muhammad Tahir, Tahir Aziz Ikram, Hassan Bajwa
2012 American Journal of Bioinformatics Research  
This article presents a comprehensive survey of the applications and the algorithms for inference of huge phylogenetic trees and also gives the reader an overview of the methods currently employed for  ...  the inference of phylogenetic trees.  ...  for Inference of Huge Phylogenetic Trees: A Review  ... 
doi:10.5923/j.bioinformatics.20120201.04 fatcat:cwskdp7b6ze6xdlq5qekgypjwm

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1

Vincent Lefort, Richard Desper, Olivier Gascuel
2015 Molecular biology and evolution  
FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ).  ...  FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange.  ...  A number of tree-building algorithms have been added, to infer an initial tree or to improve that tree (or any input tree) with topological moves.  ... 
doi:10.1093/molbev/msv150 pmid:26130081 pmcid:PMC4576710 fatcat:wx77jrvi5bctzpw6tgk7zrnspa

LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa

Carlos J. Rivera-Rivera, Juan I. Montoya-Burgos
2016 Molecular biology and evolution  
For each gene, LS 3 sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates.  ...  The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction  ...  We also acknowledge Herv e Philippe and Xiaofan Zhou for kindly providing us with their datasets.  ... 
doi:10.1093/molbev/msw043 pmid:26912812 pmcid:PMC4868118 fatcat:mfgfbbjt5nhzdgoqjt7ibp4jai

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

Clément-Marie Train, Natasha M Glover, Gaston H Gonnet, Adrian M Altenhoff, Christophe Dessimoz
2017 Bioinformatics  
Results: We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in  ...  With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.  ...  Acknowledgements We thank Georgina Bland for her contribution to the refinement for asymmetrically evolving paralogs, and Karina Zile for her thoughtful review of the article.  ... 
doi:10.1093/bioinformatics/btx229 pmid:28881964 pmcid:PMC5870696 fatcat:6nhrdpyjgjhsno5r5uwrosv64q

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

Paul D Thomas
2010 BMC Bioinformatics  
We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning much of the  ...  Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological.  ...  Acknowledgements The author is indebted to Stan Dong for implementing the comparisons between the different tree methods. This work was supported in part by NIGMS grant R01GM081084.  ... 
doi:10.1186/1471-2105-11-312 pmid:20534164 pmcid:PMC2905364 fatcat:ctzjj4py3rdttii3lrpgrtzbve

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

A. Boc, A. B. Diallo, V. Makarenkov
2012 Nucleic Acids Research  
It also comprises fast and effective methods for inferring phylogenetic trees from complete and incomplete distance matrices as well as for reconstructing reticulograms and HGT networks, including the  ...  T-REX (Tree and reticulogram REConstruction) is a web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.  ...  providing us with the source code of their methods and/or for their helpful comments.  ... 
doi:10.1093/nar/gks485 pmid:22675075 pmcid:PMC3394261 fatcat:fqnr3l3qbfhclpiyzynztdrjmm

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

Ari Löytynoja, Nick Goldman
2010 BMC Bioinformatics  
Its implementation in the PRANK alignment program package also allows modelling of complex evolutionary processes and inference of posterior probabilities for sequence sites evolving under each distinct  ...  In addition to de novo alignments, webPRANK can be used for the inference of ancestral sequences with phylogenetically realistic gap patterns, and for the annotation and post-processing of existing alignments  ...  Acknowledgements We thank Simon Whelan for the help with DNA substitution models, Tim Massingham for his critical comments and alternative ideas for visualising sequences, Nicolas Rodriguez for the formal  ... 
doi:10.1186/1471-2105-11-579 pmid:21110866 pmcid:PMC3009689 fatcat:rbtoridtofdvbkpjzk6qurrvs4

A Novel Genetic Algorithm based Approach for Optimization of Distance Matrix for Phylogenetic Tree Construction

Mridu Gupta, Shailendra Singh
2012 International Journal of Computer Applications  
The K-tuple distance approach is not effective for set of sequences which are almost identical where as F-tuple distance is useful for constructing phylogenetic tree for set of identical sequences.  ...  Phylogenies are useful for organizing knowledge of biological diversity, for structuring classifications, and for providing knowledge of events that occurred during evolution.  ...  Phylogenetics uses the structure and function of molecules and how they change over time to infer these evolutionary relationships and construct phylogenetic tree.  ... 
doi:10.5120/8229-1303 fatcat:anz63ighsvfs7mil2itmq6alae

Scelestial: fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm [article]

Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice Carolyn McHardy
2021 bioRxiv   pre-print
This creates a need for data-specific computational methods, for purposes such as for cell lineage tree inference.  ...  The objective of cell lineage tree reconstruction is to infer the evolutionary process that generated a set of observed cell genomes.  ...  Our method infers the evolutionary history for single-cell data in the form of a lineage tree and imputes the missing values accordingly.  ... 
doi:10.1101/2021.05.24.445405 fatcat:m4bzniqq75cr7f2ykx5qqxrqg4

Phylogenetic Inference with Weighted Codon Evolutionary Distances

Alexis Criscuolo, Christian J. Michel
2009 Journal of Molecular Evolution  
Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate  ...  as, if not better, than those inferred by maximum likelihood.  ...  Acknowledgments We thank Simonetta Gribaldo as well as the referees for their helpful comments and suggestions on the manuscript.  ... 
doi:10.1007/s00239-009-9212-y pmid:19308635 fatcat:mhtrtdl6kfabhezn27lh27ewpi

A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

Alexis Criscuolo
2019 Research Ideas and Outcomes  
These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch.  ...  This paper describes a novel alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences using publicly available bioinformatics tools.  ...  The author thanks Laetitia Fabre, Julien Guglielmini and Rachel Legendre for useful comments on the manuscript. The author is also grateful to Brian D. Ondov for reviewing this manuscript.  ... 
doi:10.3897/rio.5.e36178 fatcat:zlohssztavfkxia3yppwucmumy

LSHPlace: Fast phylogenetic placement using locality-sensitive hashing

DANIEL G. BROWN, JAKUB TRUSZKOWSKI
2012 Biocomputing 2013  
With these ideas, new sequences can be placed onto trees with high fidelity in strikingly fast runtimes.  ...  We adapt our recent work on phylogenetic tree inference, which uses ancestral sequence reconstruction and locality-sensitive hashing, to this domain.  ...  Acknowledgement We thank Andre Masella, Josh Neufeld and Michael Lynch for sharing data with us, and Erick Matsen for helpful conversations.  ... 
doi:10.1142/9789814447973_0031 fatcat:tngucve74vhjthcnnkrmvrx4eu

Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples [chapter]

Tamir Tuller, Hadas Birin, Martin Kupiec, Eytan Ruppin
2009 Lecture Notes in Computer Science  
The running time of these algorithms on simulated inputs with hundreds of protein families and hundreds of co-evolutionary relations was fast (up to four minutes) and it achieved an approximation ratio  ...  We show that this problem is NP-hard and present both a Fixed Parameter Tractable (FPT) algorithm, and heuristic approximation algorithms for solving it.  ...  The general algorithm for inferring ancestral states under co-evolution. B. The algorithm for partitioning the co-evolutionary graph. C.  ... 
doi:10.1007/978-3-642-04744-2_14 fatcat:epeqwgirnngcxdgjnjdlhioyka
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