ArticleGenome biology2008
Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed.
- Alignathon: a competitive assessment of whole-genome alignment methods.Genome research · 2014Article
- Realistic artificial DNA sequences as negative controls for computational genomics.Nucleic acids research · 2014Article
- Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.Molecular biology and evolution · 2014Article
- Automated reconstruction of ancient languages using probabilistic models of sound change.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Estimating empirical codon hidden Markov models.Molecular biology and evolution · 2013Article
- Simulation of molecular data under diverse evolutionary scenarios.PLoS computational biology · 2012Article
- Article
- Cactus: Algorithms for genome multiple sequence alignment.Genome research · 2011Article
- PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.BMC bioinformatics · 2011Article
- Simulation of genes and genomes forward in time.Current genomics · 2010Article
- Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.Molecular biology and evolution · 2009Article
- Article
- INDELible: a flexible simulator of biological sequence evolution.Molecular biology and evolution · 2009Article
- Fast statistical alignment.PLoS computational biology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.