Computational protocol: Molecular characterization and embryonic origin of the eyes in the common house spider Parasteatoda tepidariorum

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Protocol publication

[…] For phylogenetic analysis of Opsin homologues, candidate sequences were identified by BLAST search of the D. melanogaster Rhodopsin protein sequences against the transcriptome of P. tepidariorum []. In addition to P. tepidariorum sequences, Opsin protein sequences for a multiple sequence alignment were obtained from published sources [-] (see also Additional file : Table S2). Multiple sequence alignment was performed with MUSCLE version 3.8.31 [,]. The pylogenetic tree was inferred using the parallel version of MrBayes 3.2.4 [-] with default settings for the likelihood model and the priors for the phylogenetic model. The amino-acid substitution model was set to “Blosum” that was determined as the model best suited for the input data by the MrBayes program. […]

Pipeline specifications

Software tools MUSCLE, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Parasteatoda tepidariorum, Drosophila melanogaster
Diseases Eye Abnormalities