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We specifically concentrated on those regions that formed distinct clusters with multiple representatives from the same or different organisms because they were likely to represent evolutionarily conserved domains with functional relevance in a wide range of organisms.
Multiple representatives from each sequenced amoebozoan lineage were included to deeply sample the molecular diversity available within Amoebozoa and to assess congruence with other amoebozoan phylogenies.
Moreover, many of the orthologous groups have multiple representatives from each species, possibly due to the allowance of asymmetry in reciprocal BLAST hits.
This process is repeated until we have a putative council consisting of disagreements between some of the members (cells that have a 0 in the MoLFunC matrix) as well as multiple representatives from some proteomes.
We included multiple representatives from well supported amoebal lineages in our analysis to (a) look for congruence between our results and other amoebozoan phylogenies and (b) test whether any or all organisms described as protosteloid amoebae fell into a clade of amoebozoans that also included the myxogastrids and dictyostelids, i.e. Eumycetozoa sensu Olive [1].
Lacking a repeatable phylogenetic tree for all CydX, 53 sequences encompassing multiple representatives from each major clade of CydX in the CydABX phylogenetic tree were selected, and their DNA sequences were used as input.
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The isolated strains included multiple representatives of 36 species from the LAB genera including Enterococcus, Lactobacillus, Lactococcus, Leuconostic, Pediococcus, Streptococcus, and Weissella.
We now consider estimates that combine information across multiple representative sequences from each subtype.
Members of the GST supergene family were identified in the A. gambiae genome by BLAST searches [ 34] using multiple representative sequences from each GST class as query sequences.
This capability was especially important for this research project, as multiple representative images from CT scans and histological images for each patient were uploaded into the database.
The refinement step builds a set of core representatives by comparing the authority profiles of all members (except members from proteomes with multiple representatives) with the chief authority.
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