Dear HYPHY team,
I am having troubles with my newick trees. When I load them in tree view they look a certain way and then once sumitted to your site  at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login they are heavily modified, and dont look at all liek the original tree (in the output as well as the intial pdf avaliable...
here is an example of one of my trees...Ca as the outgroup...

(Ca,(an,(P3,di,lo),(P2,P4)),((so,se),(P6,tu,P7),(P1,th)));

Have you had this before? or do you think I am just doing something silly......apologies for wasting your time if so.
thanks for a great program
best wishes
Angie

Dear Angie,


wrote on Apr 7^th, 2005 at 10:09pm:

Dear HYPHY team, I am having troubles with my newick trees. When I load them in tree view they look a certain way and then once sumitted to your site  at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login they are heavily modified, and dont look at all liek the original tree Angie

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