標題: 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
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 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: 
起始頁: W221
結束頁: W227
顯示於類別:期刊論文


文件中的檔案:

  1. 000284148900036.pdf