ADOPS (Automatic Detection of Positively Selected Sites) is a novel software pipeline implemented with the goal of providing an automatic and flexible tool for detecting positively selected amino acid sites from a set of unaligned nucleotide sequence data.
The pipeline uses third-party well established tools to perform several steps involved in the process of detecting positively selected sites: (i) alignment of the sequences using T-coffee, (ii) inference of phylogenetic trees with MrBayes and (iii) detection of positively selected amino acid sites using codeml. ADOPS software implements a graphical user interface that provides an integrated view of all the results including intermediate stages (such as the tree used and convergence statistics).
ADOPS is ideal for research projects involving the analysis of tens of genes. Although a good and easy to use graphical interface is provided, the entire pipeline can be run using a command line option as well thus being adequate to process hundreds or thousands of genes as well. ADOPS software can be freely downloaded from http://sing.ei.uvigo.es/ADOPS/.