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RESEARCH PRODUCT
Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits
Andrés MoyaLuis DelayeAmparo LatorreCarlos Vargassubject
0303 health sciencesPhylogenetic treeCombined usemacromolecular substancesComputational biologyBiologyGenome03 medical and health sciences0302 clinical medicineMolecular evolutionPhylogeneticsIdentification (biology)GeneInferring horizontal gene transfer030217 neurology & neurosurgery030304 developmental biologydescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2020-01-01 |