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Table 7 Specific differences between FIGENIX's phylogenomic inference pipeline and other software

From: FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

FIGENIX RIO PhyloGenie
Homologous sequences search on any NCBI-formatted database including nr, Swissprot and Ensembl. Homologous sequences search limited to Swissprot and trEMBL. Homologous sequences search on any NCBI-formatted database including nr.
Choice of the scope of phylomes by the user (root = all phylomes by default) No choice of the scope of phylomes by the user. Choice of the scope of phylomes by the user.
Automatic detection of domains on the query sequence. Manual input of a domain that must be present in pfam and for which pairwise distances must have been precalculated. Phylogenetic reconstruction at BLAST's high scoring pairs (HSPs) level converted after corrections in multiple sequence alignment (MSA).
Expert system selection of domains and repeats whose evolutionary behaviour are congruent. Phylogenetic reconstruction on a single domain provided by the user. No test for domains congruence. Phylogenies constructed on a corrected alignment with a HMM profile.
When no domain is found phylogenetic reconstruction on the "alignable" portion of the query sequence. No reconstruction possible when no known domain is present on the query sequence. Phylogenetic reconstruction possible regardless the presence of a known domain on the query sequence.
Elimination of sites not evolving under neutral evolution. No elimination of sites producing biases in phylogenetic reconstruction. No elimination of sites producing biases in phylogenetic reconstruction.
Elimination of sequences having a divergent amino acids composition No elimination of sequences with divergent composition. No test for sequence composition but selection for sequences producing significant alignments with the query HMM.
Phylogenetic reconstruction with three different methods and projection on a consensus tree. Phylogenetic reconstruction with one single method (NJ). Choice of reconstruction method (NJ by default) but only one method at a time and no fusion with multiple methods.
Comparison of the consensus tree with NCBI reference tree of life containing around 200,000 taxa. Comparison of the NJ tree with a reference tree of life containing around 2,500 taxa. Comparison of the one-method tree with NCBI reference tree of life containing around 200,000 taxa.
Automatic detection of speciation and duplications, of orthologs and paralogs. Automatic detection of speciation and duplications, of orthologs and paralogs. Functionality not available. Possibility to scan a database of trees for a given topology.
Automatic extraction of experimentally verified functional information for all detected orthologs and paralogs. Functionality not available Functionality not available