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synima website  

Synima (Synteny Imager) is a program for visualising syntenic regions from orthologous genes, infered by reciprocal best hits (RBH) from BLAST, or OrthoMCL or Orthofinder, followed by DAGchainer. OrthoMCL, Orthofinder and DAGchainer are bundled with Synima, with wrapper scripts provided in /util/. Several scripts launch several jobs that can be run on a grid (LSF, GridEngine, UGER are supported).

Environment Modules

Run module spider synima to find out what environment modules are available for this application.

System Variables

  • HPC_SYNIMA_DIR - installation directory
  • HPC_SYNIMA_BIN - executable directory
  • HPC_SYNIMA_EXE - example directory


If you publish research that uses synima you have to cite it as follows:

Farrer RA (2017), BMC Bioinformatics 18:507