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phylo: update exclude.txt
Add samples that were causing the all/genome tree to be poorly rooted <https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1766006558058999?thread_ts=1765994106.057809&cid=C01LCTT7JNN>
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phylogenetic/defaults/exclude.txt

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PP_0049YFJ # This was causing all tree to not be rooted properly
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PP_0049ZYG # This was causing all tree to not be rooted properly

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