title: IMPACT: integrated multiprogram platform for analyses in ConTest.
abstract: In this paper, we introduce a new Graphical User Interface that estimates evolutionary rates on protein sequences by assessing changes in biochemical constraints. We describe IMPACT, a platform-independent (tested in Linux, Windows, and MacOS), easy to install software written in Java. IMPACT integrates the use of a built-in multiple sequence alignment editor, with programs that perform phylogenetic and protein structure analyses (ConTest, PhyML, ATV, and Jmol) allowing the user to quickly and efficiently perform evolutionary analyses on protein sequences, including the detection of selection (negative and positive) signatures at the amino acid scale, which can provide fundamental insight about species evolution and ecological fitness. IMPACT provides the user with a working platform that combines a number of bioinformatics tools and utilities in one place, transferring information directly among the various programs and therefore increasing the overall performance of evolutionary analyses on proteins.
authors.affiliation: CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.
authors.forename: Emanuel
authors.initials: E
authors.lastname: Maldonado
authors.forename: Julien Y
authors.initials: JY
authors.lastname: Dutheil
authors.forename: Rute R
authors.initials: RR
authors.lastname: da Fonseca
authors.forename: Vítor
authors.initials: V
authors.lastname: Vasconcelos
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry; D014584:User-Computer Interface
chemical_list: D011506:Proteins