config_example2.yaml

#=========================== SCORPiOs EXAMPLE CONFIGURATION FILE ============================#
##For a full description of supported settings, please take a look at SCORPiOs documentation.#


#----------------------------------------- INPUTS -------------------------------------------#

# INPUT1 - The gene trees to correct, as a single file in New Hampshire Extended (.nhx) format.
trees: data/example2/trees.nhx

# INPUT2 - The multiple sequence alignments used to build the trees, as a single fasta file.
alis: data/example2/ali.fa.gz

# INPUT3 - The genes coordinates for all duplicated species and outgroup(s).
#one file per species, in BED (.bed) format. Can also be in 'dyogen' format.
genes: data/example2/genes/genes.%s.list
genes_format: 'dyogen'

# INPUT4 - The species tree in Newick format with labelled internal nodes (ancestor names).
species_tree: data/example2/species_tree.nwk


#----------------------------------------- OUTPUTS ------------------------------------------#

# Provide a job name, which will be appended to the output folder name.
jobname: 'example2'


#---------------------------------------- PARAMETERS ----------------------------------------#

# Whole-genome duplication(s) and outgroup(s)
# Outgroups, if multiple, should be monophyletic if you intent to run LORelEi.
WGDs:
    Osteoglossocephalai: 'Amia.calva'

# Whether the average number of syntenic orthologs to include genes in the Orthology Table
# should be optimized: yes ('y') or no ('n'). Default threshold value if not optimized: 2.0.
optimize_synteny_support_threshold: 'n'

# Whether branch-lengths should be recomputed after corrections: yes ('y') or no ('n').
brlength: 'n'

# Whether more detailed intermediary outputs should be saved: yes ('y') or no ('n').
# Setting `save_subtrees_lktest` to 'y' saves, in addition to default outputs:
# - constrained tree topologies
# - profileNJ and TreeBeST synteny-aware trees
# - AU-tests outputs
# Should be set to 'y' if you intent to run LORelEi.
save_subtrees_lktest: 'y'

# Iterative-correction related option, automatically updated by the wrapper iterate_scorpios.sh.
## DO NOT MODIFY MANUALLY even if using iterative mode.##
current_iter: 0


#---------------------------------------- RESSOURCES ----------------------------------------#

# Maximum number of threads (will never use more than this number).
# It will be restricted to the number specified via --cores (1 if --cores is not invoked).
ncores: 14