Genespace synteny analysis

genespace_genomes contains translated cds .faa and genomic gff annotation files for three taxa (B. pensylvanicus, B. affinis, B. huntii) needed for the R code below. Results can be replicated by running the R code for GENESPACE (see https://github.com/jtlovell/GENESPACE for software and other requirements).<b>R-code for running Genespace:</b>library(GENESPACE)<br>genomeRepo&lt;-file.path("genespace/genespace_genomes")workdir&lt;-file.path("genespace/genespace_working")<br>parsedPaths &lt;- parse_annotations( rawGenomeRepo = genomeRepo, genomeDirs = c("affinis", "huntii", "pens"), genomeIDs = c("affinis", "huntii", "pens"), presets = "ncbi",troubleShoot = TRUE, genespaceWd = workdir)<br><br>gpar &lt;- init_genespace( wd = workdir, <br> path2mcscanx ="GenomeSoftware/MCScanX-master")out &lt;- run_genespace(gsParam = gpar) <br>