In depth guide

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In depth guide

				Comma separated value (.csv); FASTA (.fas) and Genbank (.gb) sequence files

				jbei-seq format (.xml) sequence files

				SBOL XML format (.xml) sequence files

				j5 input files

				j5 parameters file

				Sequences list file and zipped sequences file

				Parts list file

				Target part order list file

				Eugene rules list file

				Master plasmids list file

				Master oligos list file

				Master direct syntheses list file

				Assembly files to condense list file and zipped assembly files file

				Downstream automation parameters file

				Multi-well plate file

				Source plate list file and zipped source plate files file

				j5 output

			Assembly files

				SLIC/Gibson/CPEC/SLiCE

				Combinatorial SLIC/Gibson/CPEC/SLiCE

			Mock Assembly

			Combinatorial Mock Assembly

				Golden Gate

				Combinatorial Golden Gate

				Condensed multiple j5 assembly files

			Downstream automation

				Distribute PCR reactions file

				PR-PR distribute (split and pool) PCR reactions configuration (.pr) files

			Interfaces for using j5

			Integration with the JBEI Registry/Vector Editor/DeviceEditor and Clotho BioCAD platforms

				XML-RPC web services provider

				Simplified j5 web interface

				Simplified j5 SBOL XML <-> GenBank conversion utility web interface

			Stand alone command line interface

			Error messages

				List of j5 error messages