Dear sam,

In HyPhy, all taxon (and tree leaf) names must be valid programming identifiers, i.e. consist only of letters, numbers and the underscore character. Looks like you tree had 'gabonin-2' as a taxon name and HyPhy complained about the '-' character. If you replace '-' with the underscore in the tree string (and also in the alignment file), the error should disappear.

Take a look at section 2.3.2 in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for more detail.

Cheers,
Sergei

Dear sam,

'.' is also invalid (0.80 in your case). If you look at the placement of the '?' in the error message, it will be immediately FOLLOWING the offending character.

Cheers,
Sergei

Dear sam,

It looks like your original tree used a shorthand notation for bootstrap support (e.g. 0.78) and branch lengths at once. E.g. as in the following
((((((((EO5A:0.04386799,gabonin_2:0.00931429)[b]0.78:0.02439405[/b]).

HyPhy (as per the Newick format) will interpret 0.78 (or 078 with the edited '.') in the above as a taxon name. Now assume that two internal branches have 0.78 bootstrap support - this will lead to two internal branches having the same name. HyPhy complains about that because each branch needs to have a unique name so that we can refer to the branch if needed.

Try deleting these numerical values before feeding the tree into HyPhy.

Aren't the lack of format standards and ad-hoc extensions which only one or two packages understand great?

Cheers,
Sergei

Dear sam,

Either there are too few leaves in the tree, or you may have inadvertently deleted something in the tree string to shorten it. If you are using a GUI version of HyPhy, you can go to Windows->Object Inspector (or on Windows, to File->Object Inspector), select the Trees option from the menu and double click on the tree name to show a graphical view of the tree HyPhy read.

I would check your tree string for premature ')' and missing ','. You can also go back to MEGA and try to save the tree without the bootstrap support info. Finally, you can use HyPhy to build a NJ tree (the kind MEGA does) in the vanilla Newick format.

Cheers,
Sergei

Dear sam,

Which model options did you select? This error is a bit unusual - it probably suggests that the data may be very non-clock like, so much so, that the program fails to find a feasible solution. Make sure the tree is rooted correctly. If all else fails, send me the data (spond at ucsd edu), so that I can duplicate the error and diagnose the source.

Cheers,
Sergei

Dear sam,

Something strange is going on - this error is very rare; I am afraid I can't give you meaningful advice unless I can see your data and recreate the problem. I'd like to get to the bottom of this.

Sorry you are having so many difficulties... it must be frustrating.

Cheers,
Sergei

Dear sam,

Thanks to you, I discovered that I introduced a bug in HyPhy (in the last 1.5 months) which led to unwarranted error messages under certain conditions (like those found in MolecularClock.bf).

I fixed the problem in today's build (Apr 12th 2007); please download the latest version (if you are using an Intel Mac, do not use the universal binary - I will update that later today - get the older OS X version instead) and run the analyses using it.

Thanks so very much for helping me discover and eliminate this potentially serious bug!

Cheers,
Sergei