The lambda tree structure does not match that of the tree #240
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Hey ya'll, Really appreciate your work in developing/maintaining this tool! I'm running into an issue where my lambda tree doesn't seem to match the structure of my time-calibrated tree. I can run CAFE5 just fine without the --lambda-tree option. I've seen this is a point that's been discussed previously, but I'm not really sure what the fix is. I went in and edited my tree to match the format of "chimphuman_separate_lambda.txt", or so I thought. I've attached both of my trees below. Any ideas? Thank you in advance for your help! Austin |
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A word that comes directly after a close-paren is considered a node label, so you've labeled most of the nodes in your tree with "1". That should be ok, I think; but an ancestor of Sus_scrofa is actually labelled as "0.901". CAFE5 is looking for a matching label in the lambda tree and not finding it. 
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Hi Ben, Thank you for pointing this out. Totally my mistake. The node labels needed removed entirely - everything seems to be working just fine now! Thank you again, Austin |
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A word that comes directly after a close-paren is considered a node label, so you've labeled most of the nodes in your tree with "1". That should be ok, I think; but an ancestor of Sus_scrofa is actually labelled as "0.901". CAFE5 is looking for a matching label in the lambda tree and not finding it.