INDELible: a flexible simulator of biological sequence evolution (Q34979731)

5 August 2017

INDELible: a flexible simulator of biological sequence evolution (English)

1 reference

5 August 2017

William Fletcher

1

1 reference

PubMed ID

19423664

5 August 2017

Ziheng Yang

series ordinal

2

1 reference

5 August 2017

7 May 2009

1 reference

Molecular Biology and Evolution

5 August 2017

1 reference

5 August 2017

26

1 reference

5 August 2017

8

1 reference

5 August 2017

1879-1888

1 reference

Problems and solutions for estimating indel rates and length distributions

5 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Investigating protein-coding sequence evolution with probabilistic codon substitution models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Exploring tree-building methods and distinct molecular data to recover a known asymmetric phage phylogeny.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

An improved general amino acid replacement matrix

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

HIV-specific probabilistic models of protein evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

An empirical codon model for protein sequence evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

The accuracy of several multiple sequence alignment programs for proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

An initial map of insertion and deletion (INDEL) variation in the human genome.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Bayes empirical bayes inference of amino acid sites under positive selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Reconstructing large regions of an ancestral mammalian genome in silico

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Different versions of the Dayhoff rate matrix

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Estimating the frequency of events that cause multiple-nucleotide changes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Indel-based evolutionary distance and mouse-human divergence

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Majority of divergence between closely related DNA samples is due to indels

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Initial sequencing and comparative analysis of the mouse genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Codon-substitution models for heterogeneous selection pressure at amino acid sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Rose: generating sequence families.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Synonymous and nonsynonymous rate variation in nuclear genes of mammals.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

PAML: a program package for phylogenetic analysis by maximum likelihood

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Success of maximum likelihood phylogeny inference in the four-taxon case

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

On the use of nucleic acid sequences to infer early branchings in the tree of life

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Evolutionary trees from DNA sequences: A maximum likelihood approach

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Line-of-descent and genealogical processes, and their applications in population genetics models.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

5-Methylcytosine in eukaryotic DNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Estimation of evolutionary distances between homologous nucleotide sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Maximum likelihood alignment of DNA sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

An evolutionary model for maximum likelihood alignment of DNA sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

The rapid generation of mutation data matrices from protein sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Amino acid substitution matrices from protein blocks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

MtArt: A New Model of Amino Acid Replacement for Arthropoda

8 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Regional and time-resolved mutation patterns of the human genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Statistical tests of models of DNA substitution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Simulating DNA coding sequence evolution with EvolveAGene 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Experimental Phylogenetics: Generation of a Known Phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

The importance of proper model assumption in bayesian phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

A codon-based model designed to describe lentiviral evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

Models of amino acid substitution and applications to mitochondrial protein evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP098

MySSP: non-stationary evolutionary sequence simulation, including indels.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

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

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712615

Estimating the pattern of nucleotide substitution

26 October 2018

1 reference

12 December 2020

Modeling amino acid replacement

1 reference

12 December 2020

Distribution of Indel lengths

1 reference

12 December 2020

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

1 reference

12 December 2020

Patterns in spontaneous mutation revealed by human-baboon sequence comparison

1 reference

12 December 2020

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSP098

1 reference

5 August 2017

1 reference

5 August 2017

1 reference

PubMed ID

19423664