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Hi,
I would like to ask how to specify an entire clade for an outgroup in ancestral sequence reconstruction. It seems that if I use the -o flag, and provide a monophyletic clade with several species: -o species1,species2,species3, it is the first (species1) that is used as the outgroup (and the node between species1 and species2 as root), instead of using the entire clade (and the node that conects it with the rest of the tree as root). Is there a way around it, or one effectively should always provide a single taxon for the outgroup? (It seems to have a very small effect on the results though.)
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iqtree
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Hi,
I would like to ask how to specify an entire clade for an outgroup in ancestral sequence reconstruction. It seems that if I use the -o flag, and provide a monophyletic clade with several species: -o species1,species2,species3, it is the first (species1) that is used as the outgroup (and the node between species1 and species2 as root), instead of using the entire clade (and the node that conects it with the rest of the tree as root). Is there a way around it, or one effectively should always provide a single taxon for the outgroup? (It seems to have a very small effect on the results though.)
Kind regards,
G
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