Troubles rooting Mrbayes consensus tree output

[Raquel Pereira]

HI I have obtained a majority consensus tree output from MrBayes.

The I tried to root my tree but so far I have been unsuccessful.

I tried:

mbtree2<-ape::root(mbtree, outgroup = mbtree@phylo$tip.label[48], edgelabel = TRUE)

Error in `dplyr::inner_join()`: ! Can't join on `x$node` x `y$node` because of incompatible types. ℹ `x$node` is of type <character>>. ℹ `y$node` is of type <integer>>. Traceback: 1. ape::root(mbtree, outgroup = mbtree@phylo$tip.label[48], edgelabel = TRUE) 2. root.treedata(mbtree, outgroup = mbtree@phylo$tip.label[48], . edgelabel = TRUE) 3. update_data(phy@data, node_map) 4. dplyr::inner_join(data, node_map, by = c(node = "old")) %>% dplyr::select(c("new", . cn)) %>% dplyr::rename(node = .data$new) 5. dplyr::rename(., node = .data$new) 6. dplyr::select(., c("new", cn)) 7. dplyr::inner_join(data, node_map, by = c(node = "old")) 8. inner_join.data.frame(data, node_map, by = c(node = "old")) 9. join_mutate(x, y, by = by, type = "inner", suffix = suffix, na_matches = na_matches, . keep = keep) 10. join_rows(x_key, y_key, type = type, na_equal = na_equal, error_call = error_call) 11. tryCatch(matches <- vec_match(x_key, y_split$key, na_equal = na_equal), . vctrs_error_incompatible_type = function(cnd) { . rx <- "^[^$]+[$]" . x_name <- sub(rx, "", cnd$x_arg) . y_name <- sub(rx, "", cnd$y_arg) . bullets <- c(glue("Can't join on `x${x_name}` x `y${y_name}` because of incompatible types."), . i = glue("`x${x_name}` is of type <{x_type}>>.", . x_type = vec_ptype_full(cnd$x)), i = glue("`y${y_name}` is of type <{y_type}>>.", . y_type = vec_ptype_full(cnd$y))) . abort(bullets, call = error_call) . }) 12. tryCatchList(expr, classes, parentenv, handlers) 13. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 14. value[[3L]](cond) 15. abort(bullets, call = error_call) 16. signal_abort(cnd, .file)

mbtree2<-ape::root(mbtree, outgroup = c(48)) (same error as above)

mbtree2<-ape::root(mbtree, outgroup = c(45,46))

Error in root.phylo(tree, outgroup = outgroup, node = node, edgelabel = edgelabel, : the specified outgroup is not monophyletic Traceback: 1. ape::root(mbtree, outgroup = c(45, 46)) 2. root.treedata(mbtree, outgroup = c(45, 46)) 3. root(tree, outgroup = outgroup, node = node, edgelabel = edgelabel, . ...) 4. root.phylo(tree, outgroup = outgroup, node = node, edgelabel = edgelabel, . ...) 5. stop("the specified outgroup is not monophyletic")

which(mbtree@phylo$tip.label =="Amphilectus_fucorum_coxIZMAPOR1981

But they are monophyletic I've open in figtree without changing the it and they are.

mbtree2<-ape::root(mbtree, outgroup = mbtree@phylo$tip.label[c(45,46)],edgelabel = TRUE) (same error as above)

Also:

ape::root.phylo(mbtree, outgroup = outgrp): object not of class "phylo"

Error in ape::root.phylo(mbtree, outgroup = outgrp): object not of class "phylo" Traceback: 1. ape::root.phylo(mbtree, outgroup = outgrp) 2. stop("object not of class \"phylo\"")

ggtree::reroot

Error: 'reroot' is not an exported object from 'namespace:ggtree' Traceback:

I'm at lost how to solve the issue and anyhelp will be welcome

[Juan Monroy-Nieto]

I just tried it with `ape::root.phylo(x, outgroup = 48)` and it works just fine. In my experience, not class phylo should prompt you to double check that (A) you object exists. In your case you use mbtree and mbtree2 so that might be the issue and (B) that `class(mbtree)` contains "phylo".

Thank you for sharing your tree, this makes it easy to troubleshoot.