دورية أكاديمية
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
| العنوان: | AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses |
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| المؤلفون: | Mevik Bjørn-Helge, Ruden Torgeir, Enger Pål, Orr Russell JS, Skjæveland Åsmund, Kumar Surendra, Burki Fabien, Botnen Andreas, Shalchian-Tabrizi Kamran |
| المصدر: | BMC Bioinformatics, Vol 10, Iss 1, p 357 (2009) |
| بيانات النشر: | BMC, 2009. |
| سنة النشر: | 2009 |
| المجموعة: | LCC:Computer applications to medicine. Medical informatics LCC:Biology (General) |
| مصطلحات موضوعية: | Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5 |
| الوصف: | Abstract Background Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Results Here we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. Conclusion The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2105 |
| Relation: | http://www.biomedcentral.com/1471-2105/10/357; https://doaj.org/toc/1471-2105 |
| DOI: | 10.1186/1471-2105-10-357 |
| URL الوصول: | https://doaj.org/article/4df5dca048954f05acb158b8b7b6e184 |
| رقم الأكسشن: | edsdoj.4df5dca048954f05acb158b8b7b6e184 |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 14712105 |
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| DOI: | 10.1186/1471-2105-10-357 |