title: SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics.
abstract: BACKGROUND
  Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the assembly of large datasets, such as multiple copies of a gene per species (paralogous or xenologous genes), lack of some genes for a given species, or partial sequences. The use of undetected paralogous or xenologous genes in phylogenetic inference can lead to inaccurate results, and the use of partial sequences to a lack of resolution. A tool that selects sequences, species, and genes, while dealing with these issues, is needed in a phylogenomics context.
  
  
  RESULTS
  Here, we present SCaFoS, a tool that quickly assembles phylogenomic datasets containing maximal phylogenetic information while adjusting the amount of missing data in the selection of species, sequences and genes. Starting from individual sequence alignments, and using monophyletic groups defined by the user, SCaFoS creates chimeras with partial sequences, or selects, among multiple sequences, the orthologous and/or slowest evolving sequences. Once sequences representing each predefined monophyletic group have been selected, SCaFos retains genes according to the user's allowed level of missing data and generates files for super-matrix and super-tree analyses in several formats compatible with standard phylogenetic inference software. Because no clear-cut criteria exist for the sequence selection, a semi-automatic mode is available to accommodate user's expertise.
  
  
  CONCLUSIONS
  SCaFos is able to deal with datasets of hundreds of species and genes, both at the amino acid or nucleotide level. It has a graphical interface and can be integrated in an automatic workflow. Moreover, SCaFoS is the first tool that integrates user's knowledge to select orthologous sequences, creates chimerical sequences to reduce missing data and selects genes according to their level of missing data. Finally, applying SCaFoS to different datasets, we show that the judicious selection of genes, species and sequences reduces tree reconstruction artefacts, especially if the dataset includes fast evolving species.
authors.affiliation: Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de biochimie, Université de Montréal, Montréal, Québec H3C3J7, Canada. beatrice.roure@umontreal.ca
authors.forename: Béatrice
authors.initials: B
authors.lastname: Roure
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodriguez-Ezpeleta
authors.forename: Hervé
authors.initials: H
authors.lastname: Philippe
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D044708:DNA, Concatenated / Q000032:analysis; D019143:Evolution, Molecular; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D044708:DNA, Concatenated