title: ADOPS--Automatic Detection Of Positively Selected Sites.
abstract: Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.
authors: Departamento de Informática, Universidade de Vigo, Spain.
authors: David
authors: D
authors: Reboiro-Jato
authors: Miguel
authors: M
authors: Reboiro-Jato
authors: Florentino
authors: F
authors: Fdez-Riverola
authors: Cristina P
authors: CP
authors: Vieira
authors: Nuno A
authors: NA
authors: Fonseca
authors: Jorge
authors: J
authors: Vieira
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics*; D001331:Automation; D001483:Base Sequence; D040503:Coffea / Q000201:enzymology / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012260:Ribonucleases / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D000596:Amino Acids; D012260:Ribonucleases; C022542:ribonuclease S