دورية أكاديمية
ALF--a simulation framework for genome evolution.
العنوان: | ALF--a simulation framework for genome evolution. |
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المؤلفون: | Dalquen DA; Computational Biochemistry Research Group, Department of Computer Science, ETH Zurich, Universitätstrasse 6, Zürich, Switzerland. ddalquen@inf.ethz.ch, Anisimova M, Gonnet GH, Dessimoz C |
المصدر: | Molecular biology and evolution [Mol Biol Evol] 2012 Apr; Vol. 29 (4), pp. 1115-23. Date of Electronic Publication: 2011 Dec 08. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Oxford University Press Country of Publication: United States NLM ID: 8501455 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1537-1719 (Electronic) Linking ISSN: 07374038 NLM ISO Abbreviation: Mol Biol Evol Subsets: MEDLINE |
أسماء مطبوعة: | Publication: 2003- : New York, NY : Oxford University Press Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983- |
مواضيع طبية MeSH: | Evolution, Molecular* , Genome* , Models, Genetic* , Software*, Computational Biology/*methods, Algorithms ; Base Composition ; Computer Simulation ; Gene Transfer, Horizontal ; Genetic Speciation ; Mutagenesis |
مستخلص: | 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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تواريخ الأحداث: | Date Created: 20111214 Date Completed: 20120919 Latest Revision: 20211021 |
رمز التحديث: | 20231215 |
مُعرف محوري في PubMed: | PMC3341827 |
DOI: | 10.1093/molbev/msr268 |
PMID: | 22160766 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1537-1719 |
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DOI: | 10.1093/molbev/msr268 |