The order of sequence alignment can bias the selection of tree topology.

@article{Lake1991TheOO,
  title={The order of sequence alignment can bias the selection of tree topology.},
  author={James A. Lake},
  journal={Molecular biology and evolution},
  year={1991},
  volume={8 3},
  pages={378-85}
}
Sequential pairwise alignment of multiple sequences is a widely used procedure (Kruskal 1983 ). It is useful and generally successful when sequences within a set differ by relatively few substitutions. Although it is well known that differential substitution rates can artifactually bias the assessment of tree topology (Felsenstein 1978), it is not generally known that the order in which sequences are aligned can bias tree selection. To test the effect of alignment order, the classical four… CONTINUE READING