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simonpenel authored Oct 21, 2024
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Expand Up @@ -36,30 +36,7 @@ phyloXML, recPhyloXML, rooted newick (NHX tags will not be considered).

# Output examples

single gene reconciliation with species tree:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1.svg


the same gene reconciliation without the species tree:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1_bis.svg


multiple genes reconciliation:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example4.svg

example with "free living" species:

https://raw.githubusercontent.com/simonpenel/thirdkind/9eb47ce644998164ff56cc68eb765c0c8a24d389/output_examples/thirdkind_fl_example.svg

multiple gene trees reconciliation with redundant transfers. Display only 1 gene tree and the transfers in red with an opacity according to the abundance of the transfer:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example2.svg


For more examples, see the "thirdkind" software https://github.com/simonpenel/thirdkind.
For output examples, please see home page https://github.com/simonpenel/thirdkind/wiki


# Using the API:
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