{"_id":"58c10f5b2c3c720f00768bd2","user":"573592b84b0ab120000b7d44","version":{"_id":"58c10f5a2c3c720f00768b87","project":"5735936aafab441700723a50","__v":4,"createdAt":"2017-03-09T08:16:26.385Z","releaseDate":"2017-03-09T08:16:26.385Z","categories":["58c10f5a2c3c720f00768b88","58c10f5a2c3c720f00768b89","58c10f5a2c3c720f00768b8a","58c10f5a2c3c720f00768b8b","58c10f5a2c3c720f00768b8c","58c10f5a2c3c720f00768b8d","58c10f5a2c3c720f00768b8e","58c10f5a2c3c720f00768b8f","58c10f5a2c3c720f00768b90","58c10f5a2c3c720f00768b91","58c10f5a2c3c720f00768b92","58c10f5a2c3c720f00768b93","58c11574b36d8c0f006fda47","58c2cdcafc6eed3900e97640","58c2ce8afc6eed3900e97663"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"2.0.0","version":"2.0"},"parentDoc":null,"__v":0,"category":{"_id":"58c10f5a2c3c720f00768b92","project":"5735936aafab441700723a50","__v":0,"version":"58c10f5a2c3c720f00768b87","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T14:34:26.031Z","from_sync":false,"order":13,"slug":"configuration-options-compara-import","title":"Configuration Options (Compara Import)"},"githubsync":"","project":"5735936aafab441700723a50","updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-01T14:58:32.791Z","link_external":false,"link_url":"","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 ]``.