Gert-Jan,
The most parsimonious tree (or indeed a tree produced by any of the other
methods) may be different from the majority of trees retrieved after bootstrap
runs. What you should do is find the number of times your user tree was
retrieved during bootstrapping. It's not that surprising that an alternative
branching pattern is found more often when bootstrapping is performed. It is
usually unstable terminal taxa or very short internal branches that lead to
this (usually??). I have also done analyses where the organisms of interest
have been found on different locations in the tree following bootstrapping.
Hope this helps,
James
