Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in FigTree. I
read it
The package phyloch has the functions mafft() and prank() which call the
programs of the same name (two other MSA software):
http://www.christophheibl.de/Rpackages.html
phyloch has many other wrappers to system calls (mrbayes, raxml, ...)
The package dna includes a port of ClustalW:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the root
instead of 100). My guess is that it's
Hi Emmanuel,
I can read in the tree fine using read.nexus too (I've attached the file
this time).
When in FigTree, if you leave the Node Labels display at 'Node Heights',
then you will see 377 at the root of the tree. If you change this
setting to 'label', you will see that the bootstrap
Hi All,
I think I have located the problem. As usual I had experienced it before
and I found (or someone else found) a workaround - but I couldn't
remember it.
The bootstrap values ($node.label) is mixed up when I save the bootstrap
tree as a nexus file with a translation table in PAUP (this
