Filters








13,958 Hits in 4.8 sec

Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference

C. Randal Linder, Rahul Suri, Kevin Liu, Tandy Warnow
2010 PLOS Currents  
However, evaluations of the efficacy of these methods for large-scale alignment and tree estimation-required for highly accurate estimations of the Tree of Life-have lagged behind method development.  ...  To facilitate testing of large-scale alignment and phylogeny estimation methods, we have assembled a collection of web pages of (1) benchmark datasets and (2) software appropriate for creating new simulated  ...  Software for generating datasets The collection of simulation software is useful for three aspects of producing simulated datasets: generating simulated phylogenetic trees (e.g., r8s [26] and Mesquite  ... 
doi:10.1371/currents.rrn1195 pmid:21113335 pmcid:PMC2989560 fatcat:h6zwnb74vnfwnayowketgddohu

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree [article]

Frederick A Matsen and Robin B Kodner and E Virginia Armbrust
2010 arXiv   pre-print
Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is available as source code  ...  A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates  ...  unifying phylogenetic framework hampers the analysis of a large collection of samples.  ... 
arXiv:1003.5943v1 fatcat:v5rns3crfbe5dcw6g6ds3f7p6m

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

Frederick A Matsen, Robin B Kodner, E Virginia Armbrust
2010 BMC Bioinformatics  
Conclusions: Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihoodbased phylogenetics methodology practical for large collections of reads; it is freely available  ...  However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic  ...  unifying phylogenetic framework hampers the analysis of a large collection of samples.  ... 
doi:10.1186/1471-2105-11-538 pmid:21034504 pmcid:PMC3098090 fatcat:p57363gaqfd7zbnga6m3spscwe

Incomplete taxon sampling is not a problem for phylogenetic inference

M. S. Rosenberg, S. Kumar
2001 Proceedings of the National Academy of Sciences of the United States of America  
Insufficient taxon sampling is often cited as a significant source of error in phylogenetic studies, and consequently, acquisition of large data sets is advocated.  ...  To test this assertion, we have conducted computer simulation studies by using natural collections of evolutionary parameters-rates of evolution, species sampling, and gene lengths-determined from data  ...  We thank Sudhindra Gadagkar, Mark Miller, Tom Dowling, Mike Douglas, Koichiro Tamura, and two anonymous reviewers for providing useful comments on earlier versions of the manuscript.  ... 
doi:10.1073/pnas.191248498 pmid:11526218 pmcid:PMC58547 fatcat:y3rmjeazurafnngap3smh6auki

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods

Sebastian Duchêne, Robert Lanfear
2015 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees.  ...  In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect.  ...  ACKNOWLEDGMENTS SD was supported by a Francisco Joséde Caldas Scholarship from the Colombian government and by a Sydney World Scholars Award from the University of Sydney.  ... 
doi:10.1002/jez.b.22638 pmid:26173578 fatcat:tf262gby3rf3xgzuuet7oa5wxm

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso, Scott T. Kelley
2016 Microbiome  
Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic  ...  distant fungi because the sequences are hard to align accurately.  ...  Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA. 4 Institute for Systems Biology, Seattle, WA, USA. 5 Department of Pediatrics, and Department of Computer Science and Engineering  ... 
doi:10.1186/s40168-016-0153-6 pmid:26905735 pmcid:PMC4765138 fatcat:ir4hti56uneavn2wlxifb6h52y

Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?

David M. Hillis, David D. Pollock, Jimmy A. McGuire, Derrick J. Zwickl
2003 Systematic Biology  
In this case, trees are more accurately reconstructed when using more sites for fewer taxa than when using more taxa for fewer sites when the total number of nucleotides is held constant in a data set.  ...  When the number of taxa sampled per clade was increased, the interrelationships of those clades could be inferred more accurately.  ...  This research was supported by grants from the National Science Foundation (DBI-9983133), the National Institute of Health (HG-02096), and the Burroughs Wellcome Fund (BWI 1001311) to S.K.  ... 
doi:10.1080/10635150390132911 pmid:12554446 pmcid:PMC2943953 fatcat:dygvv5u6kffnvjvkxxyq3kxlhq

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Swati Patel
2013 Journal of Phylogenetics & Evolutionary Biology  
These simulations also revealed that, for certain ancient bushes, analyses of concatenated data matrices surprisingly resulted in more accurate phylogenies than gene tree reconciliation.  ...  Using simulations based upon parameters derived from empirical studies, we investigated the performance of phylogenetic analyses under different conditions to identify approaches with the greatest potential  ...  versions of the manuscript.  ... 
doi:10.4172/2329-9002.1000110 fatcat:54nlrlfhn5gnhfsu4dvawwbfey

Is Sparse Taxon Sampling a Problem for Phylogenetic Inference?

David M. Hillis, David D. Pollock, Jimmy A. McGuire, Derrick J. Zwickl
2003 Systematic Biology  
In this case, trees are more accurately reconstructed when using more sites for fewer taxa than when using more taxa for fewer sites when the total number of nucleotides is held constant in a data set.  ...  When the number of taxa sampled per clade was increased, the interrelationships of those clades could be inferred more accurately.  ...  This research was supported by grants from the National Science Foundation (DBI-9983133), the National Institute of Health (HG-02096), and the Burroughs Wellcome Fund (BWI 1001311) to S.K.  ... 
doi:10.1080/10635150309356 fatcat:wfskhf7q2zbnxf4ikql23wgbya

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

Mark N. Puttick, Joseph E. O'Reilly, Alastair R. Tanner, James F. Fleming, James Clark, Lucy Holloway, Jesus Lozano-Fernandez, Luke A. Parry, James E. Tarver, Davide Pisani, Philip C. J. Donoghue
2017 Proceedings of the Royal Society of London. Biological Sciences  
We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing  ...  Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear.  ...  We thank the other members of the Bristol Palaeobiology research group for discussion; Rob Asher (Cambridge) and Thomas Guillerme for comments on the draft manuscript.  ... 
doi:10.1098/rspb.2016.2290 pmid:28077778 pmcid:PMC5247500 fatcat:cuh5wiq6s5fi5oginsu3pwaasu

SEPP: SATé-Enabled Phylogenetic Placement

S. MIRARAB, N. NGUYEN, T. WARNOW
2011 Biocomputing 2012  
We show that SATé-boosting improves HMMALIGN+pplacer, placing short sequences more accurately when the set of input sequences has a large evolutionary diameter and produces placements of comparable accuracy  ...  Recent methods of this type include HMMALIGN+EPA, HMMALIGN+pplacer, and PaPaRa+EPA. We report on a study evaluating phylogenetic placement methods on biological and simulated data.  ...  We report on a study comparing SEPP to HMMALIGN+pplacer and PaPaRa+pplacer on a collection of simulated datasets (with 500-taxon backbone trees and alignments) and one large biological dataset with a curated  ... 
doi:10.1142/9789814366496_0024 fatcat:akixiyfeknb45nkijxrewkh5zm

GASTS: Parsimony Scoring under Rearrangements [chapter]

Andrew Wei Xu, Bernard M. E. Moret
2011 Lecture Notes in Computer Science  
Our main contribution is GASTS, an algorithm for scoring a fixed phylogenetic tree: given a tree and a collection of genomes, one for each leaf of the tree, each genome given by an ordered list of syntenic  ...  GASTS enables us to attack heretofore unapproachable problems, such as accurate ancestral reconstruction of large genomes and phylogenetic inference for high-resolution vertebrate genomes, as we demonstrate  ...  One of us used GASTS to explore patterns beyond generalized adequate subgraphs on small phylogenetic trees [23] , resulting in a collection of less constrained, yet more generally applicable configurations  ... 
doi:10.1007/978-3-642-23038-7_29 fatcat:7rd65ldpknbinb6a4iijrgp5zq

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis

Samantha J Riesenfeld, Katherine S Pollard
2013 BMC Genomics  
Results To quantify errors in metagenomic read trees, we developed MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulate a sample of shotgun reads from a gene family represented  ...  Sequence-based phylogenetic trees are a well-established tool for characterizing diversity of both macroorganisms and microorganisms.  ...  Hence, we designed a large collection of simulated shotgun metagenomic datasets (Figure 1 ) to assess the effects of read length, phylogenetic method, number of reads, and reference database size and  ... 
doi:10.1186/1471-2164-14-419 pmid:23799973 pmcid:PMC3701559 fatcat:bhh4l3e42zezradnr4jrrs6ibi

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

Adam D. Leaché, Bruce Rannala
2010 Systematic Biology  
Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under maximum parsimony, maximum likelihood, and Bayesian techniques.  ...  gene trees and gaining more accurate estimates for gene trees.  ...  Yang for help with various aspects of the research. We also thank F. Burbrink, L. Knowles, L. Kubatko, L. Liu, B.  ... 
doi:10.1093/sysbio/syq073 pmid:21088009 fatcat:2buwwcrw5jd73isdpzndunpzya

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

Alexis Criscuolo
2019 Research Ideas and Outcomes  
Analyses of both simulated and real genome datasets show that this bioinformatics procedure allows accurate phylogenetic trees to be reconstructed with fast running times, especially when launched on multiple  ...  These pairwise evolutionary distances are then used to infer a phylogenetic tree and assess a confidence support for each internal branch.  ...  Acknowledgements This manuscript is dedicated to the memory of Nicolas Joly, who helped to improve the implementation of the script JolyTree for running on multiple threads.  ... 
doi:10.3897/rio.5.e36178 fatcat:zlohssztavfkxia3yppwucmumy
« Previous Showing results 1 — 15 out of 13,958 results