Unalignable sequences and molecular evolution

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Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, methodology): “…2001; Rodrigo et al., 1994; Swofford et al., 1996), others think that there is an important loss of information upon removal of any fragment of the sequences already obtained (Aagesen, 2004; Lee, 2001) and that this practice should only be used as the last resource (Gatesy et al., 1993).”
Relationships of Endemic African Mammals and Their Fossil Relatives Based on Morphological and Molecular Evidence (2003, background): “In addition, most recent molecular analyses of Afrotheria have not explored issues regarding molecular sequence homology (Lee, 2001; Asher, 2003; but see Douady et al., 2003) and have been limited to a relatively narrow range of assumptions regarding the relative influence of certain molecular…”
Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera: Formicidae) (2003, unknown): “Although some useful information is undoubtedly discarded by this exclusion procedure (Lee 2001a), such a conservative approach reduces the chances of spurious homology assignment due to alignment errors in hypervariable regions (Lutzoni 1997; Lutzoni et al.”