Is there a R equivalent of ete3 reconcile?
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18 months ago

Is there a way to do an ete3 type of analysis to get duplication events in R? I'm specifically looking for equivalents of reconcile() and .get_descendant_evol_events()

So far, I've been working with ggtree but I kinda got stuck and had to switch to python to be able to use ete3. The main reason I want to use R for this, is because the previous analyses I did were all done in R and I'd like to maintain consistency.

ete3 bioconductor r ggtree python • 731 views
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18 months ago
acvill ▴ 340

RADTE is an R script that can utilize either NOTUNG or GeneRax outputs for phylogeny reconciliation. Note that ete3's reconcile() uses Zmasek and Eddy's algorithm and expects binary trees as input. Therefore, using RADTE with GeneRax is probably the closest you're going to get. From the GeneRax paper:

The input for GeneRax consists of a rooted, but undated binary (fully bifurcating) species tree, a set of per-family MSAs (DNA or amino-acid), and corresponding gene-to-species leaf name mappings. Several genes from the same gene family can be mapped to the same species. In addition, the user can provide initial [gene family trees], typically inferred via standard phylogenetic methods (Nguyen et al. 2015; Kozlov et al. 2019).

NOTUNG, on the other hand, requires nonbinary species trees, per their website.

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Thank you. This is a really helpful starting point. It really would have been too easy, if somebody had already adapted the algorithm,.

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