Computation of likelihood values crashes

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Loading fasta alignment of 58 sequences (2488 sites)
2. Reading file ok
3. Launch Computation of likelihood values (same error with all parameters)

What is the expected output? What do you see instead?
---------------------------------------------------------------
*                                                             *
*        COMPUTATION OF LIKELIHOOD SCORES WITH PHYML          *
*                                                             *
---------------------------------------------------------------

::Settings::

 Phyml version = 3.0
 Phyml binary = PhyML_3.0_win32.exe
 Candidate models = 88
  number of substitution schemes = 11
  including models with equal/unequal base frequencies (+F)
  including models with/without a proportion of invariable sites (+I)
  including models with/without rate variation among sites (+G) (nCat = 4)
 Optimized free parameters (K) = substitution parameters + 113 branch lengths + topology 
 Base tree for likelihood calculations = ML tree
 Tree topology search operation = BEST

::Progress::

Model        Exec. Time      Total Time      -lnL
-------------------------------------------------------------------------
ML tree for HKY+I+G is invalid.ML tree for F81+I+G is invalid. 

Computation of likelihood scores interrupted. It took 00h:00:00:01.

ML tree for TrN+I+G is invalid.F81+I+G      00h:00:02:01    00h:00:02:01    0.0000
TrN+I+G     00h:00:02:09    00h:00:03:00    0.0000
HKY+I+G     00h:00:03:05    00h:00:03:05    0.0000

What version of the product are you using? On what operating system?
jModelTest2 with Windows and Linux

Original issue reported on code.google.com by alexandr...@gmail.com on 23 Mar 2012 at 12:21

[GoogleCodeExporter]

Precision: version jModelTest 2.0.2

Original comment by alexandr...@gmail.com on 23 Mar 2012 at 12:24

[GoogleCodeExporter]

Same alignment works with jModelTest0.1

Original comment by alexandr...@gmail.com on 23 Mar 2012 at 12:25

[GoogleCodeExporter]

PhyML crashes because taxa names include parentheses characters: "(" and ")". 
These characters can be manually removed. A bug report has been sent to ALTER 
developers for dealing with these chararcters in the alignment conversion.

Original comment by DiegoDL84 on 10 Apr 2012 at 10:39

• Changed state: WontFix

[GoogleCodeExporter]

What does it mean "wontfix"? I've exactly the same problem and i removed all 
the exotic characters from the header. But it doesn't work as well...

Original comment by biani.us...@gmail.com on 25 Sep 2012 at 1:36