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Mol Phylogenet Evol. 1993 Jun;2(2):152-7.

Alignment-ambiguous nucleotide sites and the exclusion of systematic data.

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  • 1Department of Invertebrates, American Museum of Natural History, New York, New York 10024.


Molecular systematists generally rely on computer algorithms to establish the alignment of DNA sequences. However, when alignment regions are characterized by multiple insertions and deletions, these gap-filled stretches of DNA are often excised before phylogenetic reconstruction. This exclusion of systematic data is generally determined by subjective criteria. We explore a replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment. Using crocodilian and insect mitochondrial (mt) ribosomal (r) DNA as examples, we caution against the removal of sequence data prior to phylogenetic reconstruction.

[PubMed - indexed for MEDLINE]
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