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ms609 / TreeDist

Calculate distances between phylogenetic trees in R
https://ms609.github.io/TreeDist/
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When no. of tips in species tree and gene tree dont match. Adding new tips to the species tree #97

Closed Jigyasa3 closed 1 year ago

Jigyasa3 commented 1 year ago

Hi @ms609 ,

Thanks again for a great package! I am trying to run TreeDist on species tree-gene tree pair where there are multiple no. of tips in the gene tree per species.

I found the add_host_tips.R script to help add new tips of zero branch length to the species tree. But it only seems to work for a specific version of the species tree (generated from BEAST2 output) but not from IQTREE or FASTTREE. For the IQTREE and FASTREE versions of the species tree, the script generates a tree with all branch lengths equal to zero.

I was wondering if there is a workaround for this problem in TreeDist? Will it work if the no. of tips in two trees are unequal?

Regards, Jigyasa

ms609 commented 1 year ago

Dear Jigyasa,

I have been working on implementing the comparison of trees with different tips – see #92. As far as I can tell this works, but I still need to find a few hours to fully test and document the new functions.

In the meantime you can access the code at https://github.com/ms609/TreeDist/tree/differentTips

or install with devtools::install_github("ms609/TreeDist@differentTips")

Do let me know how you get on!

ms609 commented 1 year ago

This code is now on its way to CRAN as version 2.6.0; hopefully it addresses your issue. Do re-open the thread if not!