Second, the incongruence might have resulted from systematic errors, although phylogenomic analyses could sometimes improve the resolution of trees and solve difficult phylogenetic questions.
Systematic errors cannot be removed by increasing data, and, on the contrary, may grow with increased size of datasets, owing to sequence composition biases among lineages and sequence heterotachy found that both MP and ML trees supported the Gnepine hypothesis when fast-evolving positions were removed frpm a 13-locus concatenated seed plants dataset,
and obtained a sister relationship between Genetales and Pinaceae after excluding fast-evolving genes and parallel sister. In addition, got congruent and robust tree topologies supporting the gentophytes-Pinaceae clade as sister of cupressophytes when the removal of highly heterotachous genes alleviated the artifact of LBA. Moreover, different rooting will directly influence of relationsships of Gnetales , angiosperms and conifers, and discussed the anthophyte hypothesis. Explored this issue using a duplicate genes rooting in analyses of phytochrome amino acid of seed plants, and yielded trees that unite cycads and angiosperms in a clade.