By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. Over that same time span,Streptomycesaccumulated thousands of point mutations. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Using a molecular clock, we estimate that theStreptomycesbacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. For this paper, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genusStreptomyces. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. The report_area command can be used to show the area of each block.Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. Generated by: Genus(TM) Synthesis Solution 18.12-s018_1 This can be changed by using the set_time_unit and set_load_unit #> report_gates Upon export into another tool, such as PnR in Innovus, the write_sdc command can be used to automatically translate Genus constraints into a common SDC form with proper units.īy default, Genus uses picoseconds and femtofarads as units. Genus uses a subset of Synopsis' language, and has additional commands for constraining a design. If these constrains are not applied, Genus will be unable to perform timing analysis or optimization during the syn_opt stage.
Synopsis Design Constraints (SDC) can be used to supply parameters to Genus, such as timing information, drive, and loads. If it cannot find some modules, it will report which when the elaboration completes. If there are unresolved modules, Genus will search for them in the paths specified in the init_hdl_search_path attribute. If you fail to specify the tech libs, Genus will give you an error. In order to perform elaboration, the technology libraries must be read in.
#Genus ii default login time clock code
Perform high-level HDL optimization such as dead code removal.The paths can be specified in the exact same way as the library paths, with multiple being concatenated in TCL list #> elaborate Similar to the init_lib_search_path attribute, specifying the library paths, the init_hdl_search_path tells Genus where to look when reading HDL files. Note: Again, if multiple LEF files are being specified using the set_db lef_library command, they must be specified simultaneously, otherwise the new library will replace the old one. This sets the synthesis mode to Physical Layout Estimation (PLE), in which physical information is used by Genus to provide better closure with back-end tools. Note: By specifying the LEF files, Genus will automatically configure the interconnect_mode attribute from the default wireload value to ple. It is a good idea to specify the tech.lef first if you fail to do so and specify the macro.lef first, Genus will warn you. Specify all LEF files when using set_db lef_library. Note: TCL list format can be specified using If you specify them sequentially, the new value will replace the old one.Įxceptions to this exist such as read_lefs -lef and read_lefs -add_lef those accomplish the same thing as set_db. Note: If you want to specify multiple strings to an attribute in Genus, you must do so simultaneously using TCL List format. The / indicates that the attribute will be set for the root level, configuring it for the entire Genus run.
When setting the technology files, LEF files, and QRC tech files, Genus will either search an absolute filepath, or within one of the directories specified with this command. init_lib_search_path tells Genus where to search for library files. This script covers everything in the Setup section of this guide. This script is written to configure the libraries, but not the HDL search paths as they aren't necessary in this tutorial. Set qrcpath $libpath/gsclib045_all_v4.4/gsclib045/qrc/qx Set lefpath $libpath/gsclib045_all_v4.4/gsclib045/lef Set timingpath $libpath/gsclib045_all_v4.4/gsclib045/timing Set libpath /opt/local/cadence/design_kits/gpdk045/lan/flow/t1u1/reference_libs/GPDK045
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