Error(?) with site concordance factor values
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Benjamin Anderson
Jan 31, 2022, 10:17:22 PM1/31/22
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Hi,
I'm running site concordance factor analysis on my ddRAD SNP alignment using a tree obtained through SVDQuartets. My command is:
iqtree -s phylo_rand.vcf_align.nex -t qfm_mod.tre --scf 100000 -T 8 --prefix concord2
I'm using IQTree v. 2.1.3 built Apr 21 2021.
The output site concordance factors do not sum to 100 and do not seem to reflect the actual counts. I'm attaching my `concord2.cf.stat` file, and I can send the actual alignment and tree if that is helpful for reproducing the effect.
iqtree -s phylo_rand.vcf_align.nex -t qfm_mod.tre --scf 100000 -T 8 --prefix concord2
I'm using IQTree v. 2.1.3 built Apr 21 2021.
The output site concordance factors do not sum to 100 and do not seem to reflect the actual counts. I'm attaching my `concord2.cf.stat` file, and I can send the actual alignment and tree if that is helpful for reproducing the effect.
Cheers,
Ben
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