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config.yaml
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workdir: "datasmall"
# options are ["nuc", "prot"]
chartype: "nuc"
resources:
# MBs
large_memory: 16000
# cores used in monolithic tasks such as decompose and prep_backbone_alignments
cores: 4
trim_config:
# sites with less non-gap fraction than below will be removed
percent_nongap: 0.05
mainlines_config:
# target number of taxa
n: 100
# concatenation alignment length
length: 5000
apples_config:
# [FM, OLS]
method: FM
# float. (0-infinity)
filter: 0.2
# integer. (5-infinity)
base: 25
prep_config:
# cluster must have a minimum diameter
edge_thr: 0.02
# approximate cluster size (no guarantees)
cluster_size: 50
# minimum subtree alignment length
sublength: 100
# minimum fragment length
fraglength: 75
infer_config:
# [raxml-ng,iqtree,raxml-8]
method: "raxml-8"
# number of starting trees
numstart: 2
refine_config:
# contract low support branches threshold. 0.9 for iqtree -abayes
contract: 0.33
# gene occupancy threshold for inclusion
occupancy: 5