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roblanf/iqtree.sh

Created December 14, 2018 02:44
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iqtree.sh
# infer the concatentated tree with 1000 ultrafast bootstraps and an edge-linked fully-partitioned model (-p is the same as -spp from version 1.7 onwards)
iqtree -s alignment.nex -p alignment.nex --prefix concat -bb 1000 -nt AUTO
# infer the 88 single-locus trees
iqtree -s alignment.nex -S alignment.nex --prefix loci -nt 50
# calculate concordance factors
iqtree -t concat.treefile --gcf loci.treefile -s alignment.nex --scf 100 --prefix concord
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