running slow EPA algorithm

[Martin Wu]

Is there a way to run the slow EPA (Evolutionary Placement Algorithm) algorithm described in the original paper http://sysbio.oxfordjournals.org/content/60/3/291.short? It seems RAxML's option for inserting query sequences -f v only runs the fast algorithm. The fast algorithm always inserts the query sequence at the middle point of the branch and I would like to avoid that.

Thanks,

Martin

[Pierre Barbera]

Dear Martin,

the "fast" algorithm will still determine the best insertion location along the branch, just that it will only do that for a set of promising candidate branches.

I recommend that you try EPA-ng, a complete re-implementation of the old EPA that is much faster. There you can also run the algorithm without the heuristic preplacement (what makes the fast mode fast) using the "--no-heur" flag. You can find the program here: https://github.com/Pbdas/epa-ng

Feel free to keep reaching out if you need help with the program, either here or on the dedicated phylogenetic placement group: https://groups.google.com/g/phylogenetic-placement

All the best,

Pierre

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