An Integrated Perspective on Phylogenetic Workflows (Q38699412)

5 September 2017

title

An Integrated Perspective on Phylogenetic Workflows (English)

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5 September 2017

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2

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

Mark Howison

3

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

Casey W. Dunn

5

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

author name string

August Guang

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

Charles E Lawrence

4

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

publication date

5 January 2016

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Trends in Ecology & Evolution

5 September 2017

number of pages

11

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based on heuristic

inferred from page(s)

published in

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

volume

31

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

11 June 2020

issue

2

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11 June 2020

page(s)

116-126

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26775796 AND SRC:MED&resulttype=core&format=json

State-of the art methodologies dictate new standards for phylogenetic analysis

11 June 2020

cites work

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Uncertainty in homology inferences: assessing and improving genomic sequence alignment

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Alignment uncertainty and genomic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Accommodating phylogenetic uncertainty in evolutionary studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Genome-scale coestimation of species and gene trees.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

The inference of gene trees with species trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Genomes as documents of evolutionary history

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Three models for the description of language

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Head-Driven Statistical Models for Natural Language Parsing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Generative models of conformational dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

A tutorial on hidden Markov models and selected applications in speech recognition

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Evolutionary trees from DNA sequences: A maximum likelihood approach

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Modeling gene family evolution and reconciling phylogenetic discord.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Gene trees and species trees are not the same

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Chromatin elimination--an oddity or a common mechanism in differentiation and development?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Genetic consequences of programmed genome rearrangement

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Characterizing and measuring bias in sequence data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

An efficient simulator of 454 data using configurable statistical models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

ART: a next-generation sequencing read simulator.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

INDELible: a flexible simulator of biological sequence evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Rose: generating sequence families

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

GenPhyloData: realistic simulation of gene family evolution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Simulating gene trees under the multispecies coalescent and time-dependent migration

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Next-generation transcriptome assembly

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Sequence assembly demystified

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Characterization of individual polynucleotide molecules using a membrane channel

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Cheap third-generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Continuous base identification for single-molecule nanopore DNA sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

An introduction to sequence similarity ("homology") searching

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Agalma: an automated phylogenomics workflow

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

HaMStR: profile hidden markov model based search for orthologs in ESTs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

An algorithm for progressive multiple alignment of sequences with insertions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

The supermatrix approach to systematics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Toward a statistically explicit understanding of de novo sequence assembly

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Phylogeny estimation: traditional and Bayesian approaches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Gene Trees in Species Trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Gene tree discordance, phylogenetic inference and the multispecies coalescent

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Bayesian inference of species trees from multilocus data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Inferring phylogeny despite incomplete lineage sorting

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Identifying a species tree subject to random lateral gene transfer

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Unified modeling of gene duplication, loss, and coalescence using a locus tree

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Joint Bayesian Estimation of Alignment and Phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Is a new and general theory of molecular systematics emerging?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

ABySS: a parallel assembler for short read sequence data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Full-length transcriptome assembly from RNA-Seq data without a reference genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Sequence comparative analysis using networks: software for evaluating de novo transcript assembly from next-generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

CGAL: computing genome assembly likelihoods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

De novo likelihood-based measures for comparing genome assemblies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Bayesian genome assembly and assessment by markov chain monte carlo sampling.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

The discovery of structural form

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Terraces in phylogenetic tree space

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

Exact calculation of distributions on integers, with application to sequence alignment

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007

A mathematical theory of communication

7 January 2021

1 reference

https://api.crossref.org/works/10.1016/J.TREE.2015.12.007