%0 Journal Article
%T PyElph - a software tool for gel images analysis and phylogenetics
%A Ana Brandu£¿a Pavel
%A Cristian Ioan Vasile
%J BMC Bioinformatics
%D 2012
%I BioMed Central
%R 10.1186/1471-2105-13-9
%X PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplification of Polymorphic DNA) and STR (Short Tandem Repeat). The similarity between the DNA sequences is computed and used to generate phylogenetic trees which are very useful for population genetics studies and taxonomic classification.PyElph decreases the effort and time spent processing data from gel images by providing an automatic step-by-step gel image analysis system with a friendly Graphical User Interface. The proposed free software tool is suitable for researchers and students which do not have access to expensive commercial software and image acquisition devices.PyElph is an open source Python based software for gel images analysis which can be used for different molecular biology or genetics studies. The software is able to analyze genetic variations of the DNA molecules from different species or populations. PyElph analyses gel image patterns of DNA genetic markers and gene
%U http://www.biomedcentral.com/1471-2105/13/9