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mrmckain / PUG

Testing WGD placement along a species tree using gene trees.
MIT License
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How to view WGD result from output files? #4

Open Dawei-Xia opened 3 years ago

Dawei-Xia commented 3 years ago

The PUG looks like a great tool for studing WGD. However, i get 9 results files when I use demo data and a "New_File_Name.pdf"

after run "Rscript PUG_Figure_Maker.R PUG_Labeled_Species_Tree.tre PUG_SUMMARIZED_5080.txt New_File_Name.pdf", i don’t

know how to deduce WGD node ？So, could you give me some advises？ Looking forward to your reply

mrmckain commented 3 years ago

Hello,

Take a look at this figure: https://github.com/mrmckain/PUG/blob/master/Final_Orchid_WGD.pdf

The different colors of branches represent the number of duplicated genes that trace back to that lineage of origin. Interpretation of a WGD is up to you. PUG is really trying to just show where duplications are. If there are a large number of duplicates combined with other evidence (like a Ks plot), then I am usually inclined to suspect a polyploid event. The SUMMARIZED_5080.txt file has the true counts based on the labeled nodes of the Labeled_Species_Tree.

Best, Michael