Query_sequence_file_name = AdiantumPHY.txt #The query sequences that will be blast against the transcriptomes; use nucleotide for BLASTn and amino acid for tBLASTn Output_file_name = phy_out #The prelix of the output files Transcriptome_list = Adiantum_aleuticum_WCLG, Anemia_tomentosa_CQPW, Angiopteris_evecta_NHCM, Argyrochosma_nivea_XDDT, Asplenium_platyneuron_KJZG, Athyrium_filixfemina_URCP, Azolla_caroliniana_CVEG, Cheilanthes_arizonica_DCDT, Cyathea_spinulosa_GANB, Cystopteris_fragilis_LHLE, Cystopteris_protrusa_YOWV, Cystopteris_reevesiana_RICC, Dennstaedtia_sp_MTGC, Equisetum_diffusum_CAPN, Gymnocarpium_dryopteris_HEGQ, Homalosorus_pycnocarpos_OCZL, Lygodium_japonicum_PBUU, Myriopteris_eatonii_GSXD, Notholaena_montieliae_YCKE, Onoclea_sensibilis_HTFH, Ophioglossum_vulgatum_WTJG, Pityrogramma_trifoliata_UJTT, Polypodium_amorphum_YLJA, Polypodium_hesperium-A_GYFU, Polypodium_hesperium-B_IXLH, Psilotum_nudum_QVMR, Vittaria_lineata_SKYV, Woodsia_scopulina_YJJY #List of folders containing the transcriptomes that will be searched BLAST_E_value = 0.000001 #The E-value threshold NCBI_BLAST = on #If 'on', each retrieved scaffold will be blast against the NCBI database (over internet). #If 'off', this step will be skipped. #If 'only', Blue Devil will only start from this step, assuming all the blast output files already exist. #If left blank, Blue Devil will go into each transcriptome folder, grab the sequence file (assuming you have them), and then make an alignment of all the sequences. This is useful if the previous run is interrupted and you want to collect the sequences all at once. Text_filtering_keywords = none #This is an optional argument. For example, providing phy|PHY will retain every scaffold that hit 'phy' or 'PHY' in NCBI blast records; otherwise the scaffold will be discarded. #If 'none', every scaffold will be retained. SOAP = both #if 'both', both SOAP de novo and SOAP de novo trans assembloes will be queried #if 'only', only the SOAP de novo trans assembly will be queried #if 'none', only the SOAP de novo assembly will be queried #if 'assemble', assume both assemblies were queried before, start from the CAP3 assembly step