OL participated in consensus tree based on core genes.
However, in term of computational costs, the consensus tree based on core genes requires more computational time than the other methods.
This tree bears a striking resemblance to the consensus tree based on core genes, although the bootstrap values are higher in many of the branches, especially near the root.
Noteworthy is the fact that reassortment is rather common among porcine viruses (e.g., H1N2, H3N1, H1N1, and H3N2) [26], thus making it more challenging to infer their subtypes based on core gene constellation.
In any case, it should be interesting to have on the same figure the whole genome tree compared to the species tree (preferentially based on core gene phylogeny).
Construction of a phylogenetic tree based on core gene sequences only (Fig. 5) revealed that two strains (L. plantarum EGD-AQ4 and L. plantarum AY01) were not part of a larger cluster that contained all other strains.
The number of infomative sites for in silico MLST tree, pan-genome tree and consensus tree based on core gene clusters were 877 bp (10,008 total base-pairs in the seven genes), 7,699 genes (10,581 total genes) and 880,832 bp (2,868,821 bp in all core genes), respectively.
f, Clustering of cancer types based on core fitness gene similarity (left) and numbers of cancer-type core-specific fitness genes exclusive to each cancer type (right).
Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought.
In general, all previously inferred phylogenies can be separated into two categories: those based on the core genes or features, which are similar to our evolutionary phylogeny, and those based on the variable gene content or other genomic features or metabolic pathways, which are similar to our similarity phylogeny.
To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species.
