title: MANTIS: a phylogenetic framework for multi-species genome comparisons.
abstract: BACKGROUND
  Practitioners of comparative genomics face huge analytical challenges as whole genome sequences and functional/expression data accumulate. Furthermore, the field would greatly benefit from a better integration of this wealth of data with evolutionary concepts.
  
  
  RESULTS
  Here, we present MANTIS, a relational database for the analysis of (i) gains and losses of genes on specific branches of the metazoan phylogeny, (ii) reconstructed genome content of ancestral species and (iii) over- or under-representation of functions/processes and tissue specificity of gained, duplicated and lost genes. MANTIS estimates the most likely positions of gene losses on the true phylogeny using a maximum-likelihood function. A user-friendly interface and an extensive query system allow to investigate questions pertaining to gene identity, phylogenetic mapping and function/expression parameters.
  
  
  BACKGROUND
  MANTIS is freely available at http://www.mantisdb.org and constitutes the missing link between multi-species genome comparisons and functional analyses.
authors.affiliation: Laboratory of Evolutionary Genetics, Institute for Molecular Biology & Medicine, Université Libre de Bruxelles, Belgium.
authors.forename: Athanasia C
authors.initials: AC
authors.lastname: Tzika
authors.forename: Raphaël
authors.initials: R
authors.lastname: Helaers
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Michel C
authors.initials: MC
authors.lastname: Milinkovitch
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface