sequence alignments
Multiple alignments are typically generated by feeding sequences into the alignment program from the N-terminus to the C-terminus.
If the same sequences are processed from the C- to the N-terminus, a different alignment is often obtained.
Because phylogenetic trees are built from alignments, the resulting trees can also differ.
References
Martin W, Roettger M, Lockhart PJ. A reality check for alignments and trees. Trends Genet. 2007 Oct;23(10):478-80. PMID: 17825944