(Q35728068)

9 August 2017

title

Short tree, long tree, right tree, wrong tree (English)

1 reference

9 August 2017

subtitle

New acquisition bias corrections for inferring SNP phylogenies (English)

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1 reference

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1

1 reference

9 August 2017

3

Joseph Felsenstein

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author name string

Barbara L Banbury

series ordinal

2

1 reference

9 August 2017

Adrián Nieto-Montes de Oca

series ordinal

4

1 reference

9 August 2017

Alexandros Stamatakis

series ordinal

5

1 reference

9 August 2017

publication date

29 July 2015

1 reference

9 August 2017

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9 August 2017

volume

64

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9 August 2017

issue

6

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9 August 2017

page(s)

1032-1047

1 reference

Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

9 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Use of RAD sequencing for delimiting species

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Demystifying the RAD fad.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Quartet inference from SNP data under the coalescent model

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Automated reconstruction of whole-genome phylogenies from short-sequence reads

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Diversity and niche evolution along aridity gradients in north american lizards (phrynosomatidae).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Phylogenetic signal variation in the genomes of Medicago (Fabaceae).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Correcting coalescent analyses for panel-based SNP ascertainment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Special features of RAD Sequencing data: implications for genotyping

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

jModelTest 2: more models, new heuristics and parallel computing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Inferring phylogenies from RAD sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Statistics and truth in phylogenomics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

phangorn: phylogenetic analysis in R

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Resolving postglacial phylogeography using high-throughput sequencing.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Search and clustering orders of magnitude faster than BLAST

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Homoplasy and clade support

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

DendroPy: a Python library for phylogenetic computing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Rapid SNP discovery and genetic mapping using sequenced RAD markers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Bushes in the tree of life

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

MUSCLE: multiple sequence alignment with high accuracy and high throughput

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

A likelihood approach to estimating phylogeny from discrete morphological character data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Usefulness of single nucleotide polymorphism data for estimating population parameters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Novel information theory-based measures for quantifying incongruence among phylogenetic trees

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Empirical assessment of RAD sequencing for interspecific phylogeny

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Inferring ancient divergences requires genes with strong phylogenetic signals.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

Quartet MaxCut: a fast algorithm for amalgamating quartet trees

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

The impact of gene-tree/species-tree discordance on diversification-rate estimation.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

How many bootstrap replicates are necessary?

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4604835

A new species of horned lizard (genus Phrynosoma) from Guerrero, México, with an updated multilocus phylogeny

25 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYV053

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26227865

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26227865

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM-LIKELIHOOD APPROACH.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26227865

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/SYSBIO/SYV053

1 reference

9 August 2017

1 reference

9 August 2017

1 reference