标题: | SoRT(2): a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations |
作者: | Huang, Yen-Lin Huang, Chen-Cheng Tang, Chuan Yi Lu, Chin Lung 生物科技学系 生物资讯及系统生物研究所 Department of Biological Science and Technology Institude of Bioinformatics and Systems Biology |
公开日期: | 1-七月-2010 |
摘要: | SoRT(2) is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. It takes as input two or more linear/circular multi-chromosomal gene (or synteny block) orders in FASTA-like format. When the input is two genomes, SoRT(2) will quickly calculate their rearrangement distance, as well as a corresponding optimal scenario by highlighting the genes involved in each rearrangement operation. In the case of multiple genomes, SoRT(2) will also construct phylogenetic trees of these genomes based on a matrix of their pairwise rearrangement distances using distance-based approaches, such as neighbor-joining (NJ), unweighted pair group method with arithmetic mean (UPGMA) and Fitch-Margoliash (FM) methods. In addition, if the function of computing jackknife support values is selected, SoRT(2) will further perform the jackknife analysis to evaluate statistical reliability of the constructed NJ, UPGMA and FM trees. SoRT(2) is available online at http://bioalgorithm.life.nctu.edu.tw/SORT2/. |
URI: | http://dx.doi.org/10.1093/nar/gkq520 http://hdl.handle.net/11536/5188 |
ISSN: | 0305-1048 |
DOI: | 10.1093/nar/gkq520 |
期刊: | NUCLEIC ACIDS RESEARCH |
Volume: | 38 |
Issue: | |
起始页: | W221 |
结束页: | W227 |
显示于类别: | Articles |
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