Simulation of Molecular Data under Diverse Evolutionary Scenarios 英文参考文献.docVIP

Education SimulationofMolecularDataunderDiverseEvolutionary Scenarios MiguelArenas1,2 * 1Computational and Molecular Population Genetics Lab (CMPG), Institute of Ecology and Evolution, University of Bern, Bern, Switzerland, 2Swiss Institute of Bioinformatics,Lausanne,Switzerland ThisisanoriginalPLoSComputational Biologytutorial. been developed to handle very complex scenarios (e.g., [8,9]) and efficient algo- rithmshavebeenincorporatedinorderto accommodatelargedatasetsinresponseto the increasing amount of genome-wide data (e.g., [10]). Thus, the importance of simulations continues to grow in order to dealwiththesenewchallenges. slower simulations due to the need to re- calculatethematrixforeachbranch. MainSoftwareImplementations Introduction A number of programs have been developed to simulate nucleotide, codon, This study is intended for evolutionary biologists interested in strategies for the simulationofmoleculardataunderdiverse evolutionary scenarios. It begins with a briefbackgroundonsimulationapproach- and amino acid sequences evolution. Although several studies have already reviewed these software tools (e.g., [13– 17]), such revisions quickly become obso- leteduetotheemergenceofnewsimula- tors, as noted in [14]. Table 1 shows an updatedlistofuser-friendlyandcommon- ly used programs available to date. Next, the most interesting software from a practicalperspectiveisbrieflydescribed. Whenattemptingtosimulateacomplex evolutionary scenario, several programs developed under the forward-time ap- proach may be useful (see Table 1). GenomePop[18]andSFS_CODE[19]seem themostcomprehensivetoolswithimple- mentationsofpopulationstructure,demo- graphicparticularities,recombination,and selection, but they do not allow simula- tions under amino acid substitution mod- els. The programs SPLATCHE2 [9] and AQUASPLATCHE [20] are able to simu- latenucleotide dataunderspatially(using landorfreshwatermaps,respectively)and temporally explicit demographic models. A disadvanta