Gene orthology for the bryozoan cleavage project

Source scripts for establishing the orthology of Membranipora membranacea genes.

Orthology was assigned by aligning amino acid sequences of M. membranacea against annotated genes from diverse metazoans using MAFFT 7.215 (Katoh and Standley, 2013), retaining only informative portions of the alignment with GBlocks 0.91b with relaxed parameters (Talavera and Castresana, 2007) and running a Maximum Likelihood phylogenetic analysis with RAxML 8.1.17 (Stamatakis, 2014) using automatic model recognition and rapid bootstrap. Alignments were manually verified using UGENE (Okonechnikov et al., 2012). Resulting trees from the maximum likelihood analysis were rendered into cladograms using the ETE Toolkit (Huerta-Cepas et al., 2010).