Troubleshooting

Memory problems

  1. Increase the memory available to the Java virtual machine. See Bonsai installation instructions.
  2. If you are making a very large tree, use Multiple Alignment Parameters so that each pairwise alignment is not kept during guide tree construction. In the opening frame, use menu "Settings : Multiple Alignment Parameters" and uncheck "Keep Pairwise Guide Alignments". It is generally desirable to keep these alignments (for example, they are required for bootstrap calculations), but the number of pair alignments kept increases in proportion to the number of sequences squared. With sequence numbers of a few hundred this can become prohibitive.
  3. If the individual sequences are very long (more than 1,000 residues or so, usually only relevant for nucleotide sequences), use Multiple Alignment Parameters to set "Memory Efficient Alignment Algorithm". This will substantially slow down the alignment, but will dramatically reduce the amount of memory required during the alignment.


James H. Thomas, Department of Genome Sciences, University of Washington
8/24/2002