Computational protocol: Olfactory coding from the periphery to higher brain centers in the Drosophila brain

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Protocol publication

[…] Sixty aligned OR amino acid sequences of D. melanogaster were obtained from the Database of Olfactory Receptors (DOR; []. The distance matrix and the phylogenetic tree were generated using Molecular Evolutionary Genetics Analysis version 7 (MEGA7) []. Analyses were conducted using the Jones-Taylor-Thornton (JTT) matrix-based model []. The analysis involved 60 amino acid sequences. All positions containing gaps and missing data were eliminated. The evolutionary history was inferred using the neighbor-joining method []. The percentage of replicate trees in which the associated ORs clustered together in the bootstrap test (1000 replicates) is shown next to the branches []. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.The PCA and hierarchical cluster analysis were performed using MATLAB. Hierarchical cluster analysis was performed using cosine distance (Fig. ), Euclidean distance (Additional file : Figure S4, Additional file : Figure S5, Additional file : Figure S6) or correlation distance (Figs. , and Additional file : Figure S8), and Ward’s classification method. One-way ANOSIM (Bray-Curtis similarity, sequential Bonferroni correction for ties, 10,000 permutations) was done with Paleontological STatistics (PAST) software ( are given as “mean ± s.d., n number”, unless otherwise noted. […]

Pipeline specifications

Software tools MEGA, PAST
Applications Miscellaneous, Phylogenetics
Organisms Drosophila melanogaster
Diseases Epilepsy, Temporal Lobe