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.

New phylogenomic and comparative analyses provide corroborating evidence that Myxozoa is Cnidaria

“…The 128 individual alignments of 58 taxa were concatenated into a supermatrix by SCaFoS version 4.42 software using the data set assembling panel (Roure et al, 2007).…”

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

“…The 113 individual alignments of the 26 taxa were concatenated into a supermatrix by software SCaFoS version 4.42 using the data set assembling panel (Roure et al, 2007). (maxdiff) in the bipartition frequencies between the two runs is less than 0.1.…”

A Single Ancient Origin for Prototypical Serine/Arginine-Rich Splicing Factors

“…RRM domains with an E , 1e-10 were extracted and clustered on similarity using BLAST scores (Altschul et al, 1997) to yield two data sets suitable for phylogenetic analyses. Briefly, for each cluster, the RRM domain showing the highest average similarity with noncluster RRMs was selected as the most slowly evolving representative of the cluster (Roure et al, 2007). In parallel, the corresponding nonredundant set of RRM-containing proteins was assembled to allow for full-length analyses (e.g.…”