Computational Tools for Parsimony Phylogenetic Analysis of Omics Data

Phylogenetic inference and parsimony analysis.

Computational methods for integrated analysis of omics and pathway data

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix 1. GENERAL INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2. A COMPUTATIONAL PLATFORM TO MAINTAIN AND MIGRATE MANUAL FUNCTIONAL ANNOTATIONS FOR BIOCYC DATABASES 9 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Background . . . . . . . . . . . . ....

Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration

Metabolomics is a rapidly growing field consisting of the analysis of a large number of metabolites at a system scale. The two major goals of metabolomics are the identification of the metabolites characterizing each organism state and the measurement of their dynamics under different situations (e.g. pathological conditions, environmental factors). Knowledge about metabolites is crucial for th...

Computational Methods for Phylogenetic Analysis

Phylogenetics is the study of relationship among species or genes with the combination of molecular biology and mathematics. Most of the present phylogenetic analysis softwares and algorithms have limitations of low accuracy, restricting assumptions on size of the dataset, high time complexity, complex results which are difficult to interpret and several others which inhibits their widespread u...

Limitations of the evolutionary parsimony method of phylogenetic analysis.

Lake's evolutionary parsimony (EP) method of constructing a phylogenetic tree is primarily applied to four DNA sequences. In this method, three quantities--X, Y, and Z--that correspond to three possible unrooted trees are computed, and an invariance property of these quantities is used for choosing the best tree. However, Lake's method depends on a number of unrealistic assumptions. We therefor...