{"_id":"574ef818db7a820e0099b9ce","project":"5735936aafab441700723a50","__v":1,"version":{"_id":"5735936aafab441700723a53","__v":12,"project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"5735e5f2ec67f6290013ac72","version":"5735936aafab441700723a53","__v":0,"project":"5735936aafab441700723a50","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T14:34:26.031Z","from_sync":false,"order":10,"slug":"configuration-options-compara-import","title":"Configuration Options (Compara Import)"},"parentDoc":null,"user":"573592b84b0ab120000b7d44","updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-01T14:58:32.791Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":7,"body":"```\n[ORTHOGROUP]\n\tPREFIX = OG\n\tPROTEIN = .faa\n\tPROTEIN_ALIGN = [ .faa.mafft Mafft ]\n\tBLASTP = .blastp\n\tFNAFILE = .fna\n\tBOUNDEDFILE = .fba\n\tTREE = .treefix.tree.DN.branlen\n```\nContains The prefix and file-type suffices for each of the files used in the compara analysis.  For each orthogroup, there should be a single folder containing one file of each type for loading into the compara database.\n\nThe alignment method used for aligned protein files should also be specified (e.g. ``PROTEIN_ALIGN = [ .faa.mafft Mafft ]``.","excerpt":"","slug":"orthogroup-compara","type":"basic","title":"[ORTHOGROUP]"}
``` [ORTHOGROUP] PREFIX = OG PROTEIN = .faa PROTEIN_ALIGN = [ .faa.mafft Mafft ] BLASTP = .blastp FNAFILE = .fna BOUNDEDFILE = .fba TREE = .treefix.tree.DN.branlen ``` Contains The prefix and file-type suffices for each of the files used in the compara analysis. For each orthogroup, there should be a single folder containing one file of each type for loading into the compara database. The alignment method used for aligned protein files should also be specified (e.g. ``PROTEIN_ALIGN = [ .faa.mafft Mafft ]``.