Contributions to Zoology, 70 (3) (2001)Emilia Rota; Patrick Martin; Christer Erséus: Soil-dwelling polychaetes: enigmatic as ever? Some hints on their phylogenetic relationships as suggested by a maximum parsimony analysis of 18S rRNA gene sequences
Material and methods

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Alignment

Since it has repeatedly been shown that the sequence alignment may influence the phylogenetic relationships inferred from ribosomal genes (Wägele & Stanjek, 1995; Winnepenninckx & Backeljau, 1996; Erséus et al., 2000; Martin et al., 2000), we studied 18S rDNA sequence data aligned in two different ways: (1) using DCSE (De Rijk & De Wachter, 1993; De Rijk, 1995), which considers a secondary structure model; (2) using Clustal W (Thompson et al., 1994), default settings, without manual corrections. Whatever the alignment method used, some hyper-variable regions of the gene (domain 23 in particular; Van de Peer et al., 1996) were virtually impossible to align and were discarded from the final alignment.