Computational protocol: Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics

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Protocol publication

[…] We tested the ability of our venom fingerprinting method to capture inter- and intra-specific variation in venom composition and generate datasets that can be used for analyses such as assessment of similarities of venom composition and correlations with ecological or genetic data. Prior to the analysis, the datasets were trimmed to contain only polymorphic markers, i.e., we excluded markers with frequency equal to 1 as they are not informative. Final binary matrices were used to calculate peak and phenotype frequencies, and other diversity measures such as individual venom richness, i.e., total number of peaks, and the Shannon diversity index []. To analyze patterns of venom composition we calculated pairwise Bray-Curtis similarity distances [] among venom profiles and conducted multivariate analyses by means of non-metric multidimensional scaling (NMDS) []. Analyses were performed using the package vegan [] in R version 3.2.3 (R Foundation for Statistical Computing, Vienna, Austria) [] and GenAlEx 6.5b3 []. […]

Pipeline specifications

Software tools vegan, GenAlEx
Application Population genetic analysis