[Database]
port=3306
use_existing_db=0
username=FRINGE_user_test
password=f1b9735665df93783272f6a2485bc3d784c99789562c23a2e6910d0c931d4688
url=10.113.34.5
db=FRINGE_instance_test
name=test
plaza_db_version=5

[Display]
print_full_screen_debug=1

[DataDirectory]
tmp_directory=
use_caching=1

[BLAST]
BLAST_RUN=1
proteome_remove_prot_ne=1
proteome_remove_internal_stop=1
blast_method=diamond
evalue=1e-05
blast_hits=1250
blast_hits_ortho=1250
blast_diamond_cores=8
blast_diamond_memory=4
blast_diamond_parallel_instances=4

[Gene_families]
GENE_FAMILIES_RUN=1
code=1237GF
remove_invalid_ORTHO=0
orthofamily_algorithm=orthofinder
overlap_ORTHO=0.95
mcl_memory=64

[OrthoFinder]
memory_multiplier=0.4
num_cores=4

[Msa_Trees]
MSA_TREES_RUN=1
aln_method=mafft
aln_method_cmd=--maxiterate 1000
perform_msa_stripping=1
perform_msa_stripping_genes=0
perform_msa_stripping_genes_divergent=0
perform_msa_stripping_genes_partial=0
perform_msa_stripping_positions=1
perform_msa_stripping_positions_maxgap=0.1
perform_msa_stripping_positions_percentile=50
perform_msa_stripping_positions_blosum=BLOSUM62
perform_msa_stripping_positions_percodon=1
perform_msa_stripping_positions_minlength=50
msa_tree_memory=5
msa_tree_cpu=30
msa_tree_minsize=3
msa_tree_maxsize=1000
tree_bs=1000
tree_method=fasttree
tree_method_cmd=-wag -gamma

[colinearity]
COLINEARITY_RUN=1
iadhore_path=i-adhore
experiment_id=1
experiment_description=default experiment
iadhore_cpu=8
memory=8
gf_type=HOM
alignment_method=gg2
gap_size=30
tandem_gap=30
cluster_gap=35
q_value=0.85
prob_cutoff=0.01
anchor_points=5
level_2_only=true
multiple_hypothesis_correction=FDR
perform_dating=0
default_ks=2
default_kn=2
default_4dtv=0.05
dating_chunk_size=500
dating_max_jobs=50

[IntegrativeOrthology]
INTEGRATIVE_ORTHOLOGY_RUN=1

[FunctionalOntology]
FUNCTIONAL_ONTOLOGY_RUN=0
go_ontology=http://purl.obolibrary.org/obo/go/go-basic.obo
interpro_ontology=https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro.xml.gz
go_evidence_scores=4:EXP,IDA,IPI,IMP,IGI,IEP|3:ISS,ISO,ISA,ISM,IGC,IBA,IBD,IKR,IRD,RCA|2:TAS,NAS|1:IC,ND,IEA

[GoProjection]
GO_PROJECTION_RUN=1
interpro_annotations_clear_db=0
go_annotations_clear_db=0
go_projection_clear_db=0
go_projection_project_parental_terms=0
go_projection_input_evidence_codes=EXP,IDA,IPI,IMP,IGI,IEP,TAS,IC
go_projection_result_evidence_code=IEA
go_projection_projection_types=FROM_TREE,FROM_IORTHO
go_projection_projection_serial=1
go_projection_family_min_percentage=0.5
go_projection_family_background=ALL
go_projection_iortho_types=TROG,ORTHO,BHIF
go_projection_iortho_num_types=2
go_projection_trog_gf_types=HOMFAM
go_projection_family_gf_types=HOMFAM
go_projection_trog_clades=Mesangiospermae
go_projection_trog_min_bootstrap=70
go_projection_trog_duplication_cutoff=0.3

[GeneFamilyEnrichment]
GF_ENRICHMENT_RUN=1
gf_enrichment_pvalue_cutoff=0.01
gf_enrichment_gf_types=HOMFAM,ORTHOFAM
gf_enrichment_minimum_coverage=50

[GeneOntologyAnnotation]
GO_ANNOTATION_RUN=1

[IdMapping]
ID_MAPPING_RUN=1
id_mapping_file=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz

[InterProScan]
INTERPRO_RUN=1
iprscan_applications=SUPERFAMILY,Gene3D,ProSitePatterns,Pfam
iprscan_golookup=1
iprscan_chunksize=300
iprscan_memory=4
iprscan_max_parallel_jobs=60
iprscan_num_cores=2
iprscan_md5lookup=0

[FunctionalClusters]
FUNCTIONAL_CLUSTERS_RUN=1
fc_data_type_1=GO
fc_tandem_1=0
fc_data_type_extra_1=PRIMARY
fc_settings_1=2,30,80,0.001,50,t
fc_data_type_2=GO
fc_tandem_2=1
fc_data_type_extra_2=PRIMARY
fc_settings_2=2,30,80,0.001,50,t
fc_data_type_3=INTERPRO
fc_tandem_3=0
fc_settings_3=2,30,80,0.001,50,t
fc_data_type_4=INTERPRO
fc_tandem_4=1
fc_settings_4=2,30,80,0.001,50,t
fc_experiments=1,2,3,4

[FunctionalAnnotation]
ath_option=genomestore_copy
bra_option=genomestore_copy
osa_option=genomestore_copy