期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 29, 期 4, 页码 1115-1123出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msr268
关键词
simulation; genome evolution; codon models; indel; lateral gene transfer; GC-content amelioration
资金
- ETH Zurich
- Swiss Science Foundation [31003A/127325]
- Swiss Institute of Bioinformatics
- Swiss National Science Foundation (SNF) [31003A_127325] Funding Source: Swiss National Science Foundation (SNF)
In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algorithms. However, current simulation packages tend to focus either on gene-level aspects of genome evolution such as character substitutions and insertions and deletions (indels) or on genome-level aspects such as genome rearrangement and speciation events. Here, we introduce Artificial Life Framework (ALF), which aims at simulating the entire range of evolutionary forces that act on genomes: nucleotide, codon, or amino acid substitution (under simple or mixture models), indels, GC-content amelioration, gene duplication, gene loss, gene fusion, gene fission, genome rearrangement, lateral gene transfer (LGT), or speciation. The other distinctive feature of ALF is its user-friendly yet powerful web interface. We illustrate the utility of ALF with two possible applications: 1) we reanalyze data from a study of selection after globin gene duplication and test the statistical significance of the original conclusions and 2) we demonstrate that LGT can dramatically decrease the accuracy of two well-established orthology inference methods. ALF is available as a stand-alone application or via a web interface at http://www.cbrg.ethz.ch/alf.
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