Cladocopium_alignments

Alignments utilised in Incongruence Length Difference and Approximately Unbiased tests. This repository contains the data used for the tests described in the study 'Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts' (JI Brian, SK Davy, SP Wilkinson) To avoid confusion by producing a multitude of files, there are six datasets, containing all sequences from the cob, ITS2 and psbAncr gene regions for samples taken from Atauro Island and Timor. From these six datasets, sequences can be easily manipulated to produce the specific datasets used in each individual test. For example, for the BBR Incongruence Length Difference test, one would concatenate the ‘cobatauro.nex’, ‘ITS2atauro.nex’ and ‘psbAatauro.nex’ files and only keep sequences beginning with ‘BBR.’ For the BBR Approximately Unbiased test, one would simply delete all non-BBR sequences from the files ‘cobatauro.nex’, ‘ITS2atauro.nex’ and ‘psbAatauro.nex’, and use the modified three files as input to PAUP*.