Selection, Concatenation and Fusion of Sequences


As the resolution of difficult phylogenetic questions needs to deal with large amounts of genes and species, the selection of sequences becomes an unavoidable step in phylogenomic studies. Furthermore, tree reconstructions are sensitive to various phenomena like gene composition, species sampling and missing data; in particular, the existence of paralogous genes and the long branch attraction artefact could create important mistakes in the phylogeny. SCaFoS is a tool that allows the selection of sequences, species and genes and the construction of various datasets taking into account previously named constraints. SCaFoS attempts to address an easy-to-use graphical interface as well a command line interface to allow anyone a large use in various biological fields that deal with multiple aligned sequences files of proteins or nucleic acids.


If you use SCaFoS, the following citation will be greatly appreciated. Please cite with:

ROURE B., RODRIGUEZ-EZPELETA N. and PHILIPPE H. SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomicsBMC Evolutionary Biology 2007, 7(Suppl 1):S2.

The paper is freely available at the BioMed Central web site


Hervé PHILIPPE's Lab