Friday, 2020-02-28 BioInfo Pakistan
Section categories
 Related Subjects [38]This category includes brief overview of all related subjects. Defining BioInformatics [7]In this section we tried to briefly explain what bioinformatics is ? Unviersities [30]This contains information about universities that are offering bioinformatics degree programs. Resources [24]Contains information about bioinformatics resources including databases, tools and techniques. Algorithms [31]This category includes some of the basic algorithms that are usually used by bioinformaticians.
 Our poll Pakistani Student Yes No Total of answers: 0
 Chat Box Only authorized users can post messages
 Statistics Total online: 1 Guests: 1 Users: 0
Home » 2011 » August » 23 » UPGMA
3:56 PM
UPGMA

 UPGMA (Unweighted group method with arithmetic mean)1. Description:   UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a simple agglomerative or hierarchical clustering method used in bioinformatics for the creation of phenetic trees (phenograms). UPGMA assumes a constant rate of evolution (molecular clock hypothesis), and is not a well-regarded method for inferring relationships unless this assumption has been tested and justified for the data set being used. UPGMA was initially designed for use in protein electrophoresis studies, but is currently most often used to produce guide trees for more sophisticated phylogenetic reconstruction algorithms.   The algorithm examines the structure present in a pairwise distance matrix (or a similarity matrix) to then construct a rooted tree (dendrogram).   At each step, the nearest two clusters are combined into a higher-level cluster. The distance between any two clusters A and B is taken to be the average of all distances between pairs of objects "x" in A and "y" in B, that is, the mean distance between elements of each cluster:   The method is generally attributed to Sokal and Michener. Fionn Murtagh found a time optimal O(n2) time algorithm to construct the UPGMA tree.2. Key Points:Sequential clustering algorithmStart with things most similarBuild a composite OTU(Operational Taxonomic Units)Distances to this OTU are computed asarithmetic means– From new group of OTUs, pick pair withhighest similarity etc.Average-linkage clustering3. UPGMA Visually:4. UPGMA Example:5. UPGMA Weaknesses:In fact, exact fitting tree exists !UPGMA assumes that the rates of evolutionare the same among different lineagesIn general, should not use this method forphylogenetic tree reconstruction (unlessbelieve assumption)Produces a rooted treeAs a general clustering method (as wediscussed in an earlier lecture), it is better…
Category: Algorithms | Views: 2853 | Added by: Ansari | Rating: 0.0/0