README

This is the alignment used for the publication:
Merrick Ekins, Dirk Erpenbeck, Gert Wörheide & John N.A. Hooper
"Deep Water Polymastiidae (Porifera, Polymastiida) from the South West Pacific."

Zootaxa (in press)

The 28S C-region sequences were generated in the course of earlier analyses as published in the Sponge Barcoding Database  and given in bold, aligned with other published polymastiid sequences using MAFFT with default settings. After each step the alignments were re-inspected for obvious alignment artefacts by eye. To add stringency GBLOCKS (Castresana 2000) was employed to remove ambiguously alignable (settings: allowing smaller blocks and gap positions in the final blocks with less strict flanking positions). See publication for more details.