πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (Q33608350)

28 July 2017

title

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (English)

1 reference

28 July 2017

5

Andrew Rambaut

0 references

Philippe Lemey

2

Philippe Lemey

0 references

Filip Bielejec

1

Filip Bielejec

0 references

Guy Baele

4

Guy Baele

0 references

Luiz Max Carvalho

3

Luiz Max Carvalho

0 references

Marc A. Suchard

6

Marc A Suchard

1 reference

28 July 2017

publication date

7 May 2014

1 reference

28 July 2017

1 reference

28 July 2017

volume

15

1 reference

28 July 2017

page(s)

133

1 reference

Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

28 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Protein evolution along phylogenetic histories under structurally constrained substitution models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Simulation of molecular data under diverse evolutionary scenarios

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Bayesian phylogenetics with BEAUti and the BEAST 1.7

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Computer simulations: tools for population and evolutionary genetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

ALF--a simulation framework for genome evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Ancient hybridization and an Irish origin for the modern polar bear matriline

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Purifying selection can obscure the ancient age of viral lineages

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Among-site rate variation and its impact on phylogenetic analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Bayesian random local clocks, or one rate to rule them all

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

FLU, an amino acid substitution model for influenza proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Phylogeography takes a relaxed random walk in continuous space and time

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Coalescent simulation of intracodon recombination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Bayesian phylogeography finds its roots

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

INDELible: a flexible simulator of biological sequence evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

GENOMEPOP: a program to simulate genomes in populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

An improved general amino acid replacement matrix

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

HIV-specific probabilistic models of protein evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

PAML 4: phylogenetic analysis by maximum likelihood

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Relaxed phylogenetics and dating with confidence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

SIMPROT: using an empirically determined indel distribution in simulations of protein evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

HyPhy: hypothesis testing using phylogenies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Rose: generating sequence families.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

A codon-based model of nucleotide substitution for protein-coding DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

The rapid generation of mutation data matrices from protein sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Amino acid substitution matrices from protein blocks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Computational reconstruction of ancestral DNA sequences

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2105-15-133

Statistical tests of models of DNA substitution.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2105-15-133

DNA assembly with gaps (Dawg): simulating sequence evolution.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

MtArt: A New Model of Amino Acid Replacement for Arthropoda

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4020384

Modeling amino acid replacement

30 October 2018

1 reference

12 December 2020

MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies

1 reference

12 December 2020

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

1 reference

12 December 2020

Model of amino acid substitution in proteins encoded by mitochondrial DNA

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-15-133

1 reference

journals/bmcbi/BielejecLCBRS14

28 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

28 July 2017

1 reference