Title: SoRT(2): a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations
Authors: 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
Issue Date: 1-Jul-2010
Abstract: 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
Journal: NUCLEIC ACIDS RESEARCH
Volume: 38
Issue: 
Begin Page: W221
End Page: W227
Appears in Collections:Articles


Files in This Item:

  1. 000284148900036.pdf