Hi all,
The current version of ape on CRAN (5.4) has a bug in its function
boot.phylo: all returned values are 0. The bug has been fixed; however,
because it was in ape's internal C code, this requires a complete
reinstallation of the package. A new version of ape with the version
number 5.4-1 is in preparation and will be submitted to CRAN in the next
few days.
In the mean time, it is possible to get the correct bootstrap values
using the bootstrap trees and the function prop.clades:
out <- boot.phylo(phy, ......, trees = TRUE)
prop.clades(phy, out$trees)
where 'phy' is the estimated tree.
A testing version of ape with the fix is available on ape-package.ird.fr.
Best,
Emmanuel
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