Delaye L, Vargas C, Latorre A, Moya A. Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits.
Methods Mol Biol 2020;
2075:355-369. [PMID:
31584175 DOI:
10.1007/978-1-4939-9877-7_25]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT.
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