ghost-tree
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JTFouquier
creating hybrid-gene phylogenetic trees for diversity analyses
ghost-tree output files should be in a folder (this might be a better option than the user selecting a name for all of their files...).
add an image displaying the grafting of the extension trees to foundation. This helped me visualize it a lot...
This shouldn't be an issue in practice as the emphasis is tree structure and branch length. However, the following situation is at least possible, and could lead to sequences in...
One thing we could try here would be to add a multiplicative factor to the cli that gives users the ability to multiply branches in the extension tree by that...
From @rob-knight: > it might be worth testing how bad it is if you graft onto the wrong name: with unifrac it’s probably not that bad so you might consider...
Suggestion from D.M.: unnecessarily O(N*M), where N is the number of sequences in the foundation alignment, and M is the number of genus level names. It probably can be reduced...
Suggestion from D.M.: line 126, which determines most_common_genus is doing a list lookup for each name, so the runtime of it is O(N \* M) where N is the number...
Test different databases (not UNITE and SILVA) for broad use of ghost-tree
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creating hybrid-gene phylogenetic trees for diversity analyses