Dear Angie,

Quote:


HyPhy may automatically reroot the trees in a way that allows it to compute likelihood functions faster. For all the analyses on datamonkey (and gabranch) we use time-reversible models of substitution, for which the rooting of the tree is immaterial (as shown in the classic Felsenstein 1981 paper). What you are seeing, therefore, should be a rerooted version of the tree you have submitted, and for all analytical purposes, it should be the same as the one you included in the data file.

Alternatively, if HyPhy was unable to read the tree (perhaps because of file format issues, or because it could not match sequence names to tip labels in the tree), then you may be seeing a Neighbor Joining tree. On the first page you see after uploading the data (the one that has data file information), make sure you see a 'User tree' option at the bottom; if this option is unavailable, look for diagnostic messages on the page (e.g. 'could not match leaf x to any sequences in the data' etc).

HTH,
Sergei