(Q34240078)

31 July 2017

ALF--a simulation framework for genome evolution (English)

1 reference

31 July 2017

4

1 reference

31 July 2017

Daniel A Dalquen

1

1 reference

PubMed ID

22160766

31 July 2017

Maria Anisimova

series ordinal

2

1 reference

PubMed ID

22160766

31 July 2017

Gaston H Gonnet

series ordinal

3

1 reference

31 July 2017

8 December 2011

1 reference

Molecular Biology and Evolution

31 July 2017

1 reference

31 July 2017

29

1 reference

31 July 2017

4

1 reference

31 July 2017

1115-1123

1 reference

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Markov models of amino acid substitution to study proteins with intrinsically disordered regions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

OrthoInspector: comprehensive orthology analysis and visual exploration

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Simulating sequences of the human genome with rare variants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

TreesimJ: a flexible, forward time population genetic simulator

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Lateral genetic transfer: open issues

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

INDELible: a flexible simulator of biological sequence evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Phylogenetic and functional assessment of orthologs inference projects and methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Algorithm of OMA for large-scale orthology inference

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Investigating protein-coding sequence evolution with probabilistic codon substitution models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

A flexible forward simulator for populations subject to selection and demography

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Fregene: simulation of realistic sequence-level data in populations and ascertained samples

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

The conditioned reconstructed process

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

An improved general amino acid replacement matrix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Evolution of protein domain promiscuity in eukaryotes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Sequence-level population simulations over large genomic regions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

An empirical codon model for protein sequence evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Calibrating a coalescent simulation of human genome sequence variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

simuPOP: a forward-time population genetics simulation environment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Empirical codon substitution matrix

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

SelSim: a program to simulate population genetic data with natural selection and recombination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Chromosome rearrangements in evolution: From gene order to genome sequence and back

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Generating samples under a Wright-Fisher neutral model of genetic variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

The evolutionary fate and consequences of duplicate genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Darwin v. 2.0: an interpreted computer language for the biosciences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Rose: generating sequence families.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

PAML: a program package for phylogenetic analysis by maximum likelihood

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Amelioration of bacterial genomes: rates of change and exchange

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

A Hidden Markov Model approach to variation among sites in rate of evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

The rapid generation of mutation data matrices from protein sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Exhaustive matching of the entire protein sequence database

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

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

6 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

In silico sequence evolution with site-specific interactions along phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

Exact stochastic simulation of coupled chemical reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

An improved algorithm for matching biological sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

Simulating DNA coding sequence evolution with EvolveAGene 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

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%2FMSR268

CS-PSeq-Gen: simulating the evolution of protein sequence under constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSR268

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=3341827

Hetero: a program to simulate the evolution of DNA on a four-taxon tree.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341827

Distribution of Indel lengths

28 October 2018

1 reference

12 December 2020

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

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

A simulation test bed for hypotheses of genome evolution

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSR268

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

22160766