As further sequences became available and phylogenetic inference grew more-sophisticated, trees were inferred for numerous gene families.
Maximum likelihood trees were inferred for each gene with PHYML v. 3.0.1 (Guindon and Gascuel 2003).
Pollen donors were inferred for 194 offspring of four adult trees using five microsatellite loci and an exclusion process.
Maximum likelihood (ML) phylogenetic trees were inferred for DWV, BQCV and IAPV.
Phylogenies were inferred for the concatenated sequences of the housekeeping genes and, individually, for the IGS, ospA and ospC.
Ancestral DNA character states were inferred for the most basal tree node using one Asian isolate (accession number AY102034) as an outgroup.
BLAST-based kingdom assignments were inferred for all ORFs occurring on the same scaffolds as the viral proteins of host origin.
GO categories were inferred for the core and auxiliary genes in strain M1 through the alignment of translated sequences against Uniprot meeting the similarity criterion of at least 50% identity covering at least 50% of both sequences.
Two break points were inferred for aexU at 153 bp and 349 bp, and gyrB at 249 bp and 528 bp, all at a significance of p<0.01 for the KH test.
Potential biological mechanisms were inferred for a number of these novel positive pairs, including nip100Δsac1Δ, in which nip100 (YPL174C) is a known component of the dynactin complex that is taking part, for instance, in chromatid separation during anaphase [47].
Haplotypes were inferred for whole chromosomes ignoring pedigree information.
