Louvard_2022_Saccularina-magnacetabula_Alignments
Description
Sequence alignments of the ITS2 and 28S rDNA sequences analysed in the manuscript "First elucidation of a didymozoid life cycle: Saccularina magnacetabula n. gen. n. sp. infecting an arcid bivalve" (Louvard, Cutmore, Yong, Dang & Cribb in press).
Files
Steps to reproduce
The ITS2 and 28S sequences produced in the study were aligned with those retrieved from GenBank (see Table 3 in the published paper) using MUSCLE v3.7 (Edgar, 2004), accessed through the CIPRES portal (https://www.phylo.org/) for ITS2 and through MEGA7 for 28S. Parameters on the CIPRES portal: -Produce a log file containing the command line: yes -Sequence weighting scheme for iteration 1: ClustalW -Clustering for iterations 1 and 2: UPGMA -Clustering method for later iterations: UPGMB -Specify output formats, fasta output. All other parameters as default. Parameters on MEGA7: -Gap open: -400 -Gap extend: -100 -Clustering method for iterations 1 and 2: UPGMA. All other parameters as default. Both alignments were trimmed on MEGA7 to the maximal length of the 50% shortest sequences. In-partition gaps were removed if affecting >25% of sequences. The alignments were further curated using Gblocks v.0.91b with parameters of least-stringent selection.