Assessing approaches for inferring species trees from multi-copy genes (Q41650098)

6 October 2017

title

Assessing approaches for inferring species trees from multi-copy genes (English)

1 reference

6 October 2017

2

1 reference

6 October 2017

3

J Gordon Burleigh

1 reference

6 October 2017

4

David Fernández-Baca

1 reference

6 October 2017

Ruchi Chaudhary

1

1 reference

6 October 2017

publication date

23 December 2014

1 reference

6 October 2017

1 reference

6 October 2017

volume

64

1 reference

6 October 2017

issue

2

1 reference

6 October 2017

page(s)

325-339

1 reference

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

6 October 2017

cites work

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Genome-scale coestimation of species and gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

iGTP: a software package for large-scale gene tree parsimony analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Fast local search for unrooted Robinson-Foulds supertrees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Gene tree parsimony vs uninode coding for phylogenetic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Reconstruction of ancient molecular phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

BEST: Bayesian estimation of species trees under the coalescent model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Estimating species trees from unrooted gene trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Coalescent methods for estimating phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Inferring phylogeny despite incomplete lineage sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Phylogenetic MCMC algorithms are misleading on mixtures of trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Resolution of ray-finned fish phylogeny and timing of diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

A bias in ML estimates of branch lengths in the presence of multiple signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

TOPD/FMTS: a new software to compare phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

A Bayesian approach for fast and accurate gene tree reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Inferring angiosperm phylogeny from EST data with widespread gene duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

How should species phylogenies be inferred from sequence data?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

DendroPy: a Python library for phylogenetic computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

A simulation study comparing supertree and combined analysis methods using SMIDGen

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Consistency properties of species tree inference by minimizing deep coalescences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

From gene trees to species trees II: species tree inference by minimizing deep coalescence events

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

The gene evolution model and computing its associated probabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093/SYSBIO/SYU128

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYU128

1 reference

6 October 2017

1 reference