QuickJoin--fast neighbour-joining tree reconstruction
نویسندگان
چکیده
منابع مشابه
QuickJoin - fast neighbour-joining tree reconstruction
We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm-while still constructing the same tree as the original neighbour-joining algorithm-making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree ne...
متن کاملSpeeding Up Neighbour-Joining Tree Construction
A widely used method for constructing phylogenetic trees is the neighbour-joining method of Saitou and Nei. We develope heuristics for speeding up the neighbour-joining method which generate the same phylogenetic trees as the original method. All heuristics are based on using a quad-tree to guide the search for the next pair of nodes to join, but differ in the information stored in quad-tree no...
متن کاملRapid Neighbour-Joining
The neighbour-joining method reconstructs phylogenies by iteratively joining pairs of nodes until a single node remains. The criterion for which pair of nodes to merge is based on both the distance between the pair and the average distance to the rest of the nodes. In this paper, we present a new search strategy for the optimisation criteria used for selecting the next pair to merge and we show...
متن کاملFast k nearest neighbour search for R-tree family
A simpliied k nearest neighbour (knn) search for the R-tree 6] family is proposed in this paper. This method is modiied from the technique developed by Roussopoulos et al. 10]. The main approach aims to eliminate redundant searches when the data is highly correlated. We also describe how MINMAXDIST calculations can be avoided using MINDIST as the only distance metric which gives a signiicant sp...
متن کاملInference of Large Phylogenies Using Neighbour-Joining
The neighbour-joining method is a widely used method for phylogenetic reconstruction which scales to thousands of taxa. However, advances in sequencing technology have made data sets with more than 10,000 related taxa widely available. Inference of such large phylogenies takes hours or days using the Neighbour-Joining method on a normal desktop computer because of the O(n) running time. RapidNJ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bth359