Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Abstract

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally-executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey. org, and the underlying codebase is available from https://github.com/veg/datamonkey-js.

Phylogenetic analysis of haemagglutinin gene deciphering a new genetically distinct lineage of canine distemper virus circulating among domestic dogs in India

“…Selection pressure analysis to test the rate of non‐synonymous (dN) to synonymous (dS) ratio (dN/dS) within H gene of CDV was estimated in Datamonkey web server (http://www.datamonkey.org/) (Weaver et al, ) using several codon‐specific models: Single‐Likelihood Ancestor Counting (SLAC), Fixed‐Effect Likelihood (FEL) and Internal Branches Fixed‐Effect Likelihood (IFEL) methods. Values of dN‐dS, “<0”, “=“and “>0” indicate negative, neutral and positive selection respectively.…”

Phylogeographic characteristics of hypervariable regions in the mitochondrial genome of a cosmopolitan, bloom‐forming raphidophyte, Heterosigma akashiwo

“…), all in the HYPHY package (Weaver et al. ), implemented at the Web‐server Datamonkey (http://www.datamonkey.org) were adopted. BUSTED is designed to identify gene‐wide evidence for episodic positive selection, whereas FUBAR and MEME identify putative selection at the level of individual sites.…”

Intra‐strain biological and epidemiological characterization of plum pox virus

“…While no significant selection bias was detected in the PIPO, five amino acid residues in the large ORF appeared to be subjected to significant positive selection (Table ). This result was supported by positive selection analyses using fixed effects likelihood (FEL) (Pond and Frost, ), single‐likelihood ancestor counting (SLAC) (Pond and Frost, ), and fast unbiased Bayesian approximation (FUBAR) (Murrell et al , ) available on the Datamonkey server (http://www.datamonkey.org/) (Weaver et al , ) (Table ). Two of these positively selected residues (amino acid positions 2,303 and 2,635) were located in nuclear inclusion protein b (NIb), a potyvirus RNA‐dependent RNA polymerase.…”