[Bioperl-l] DNAStatistics

Sarah Kingan sarahdoom at gmail.com
Mon Oct 18 11:20:25 EDT 2010


Hello,
I am trying to calculate Ka/Ks statistics using the
Align:DNAStatistics module. When I use the function, calc_KaKs_pair, I
get a long list of errors. The calculation is performed but I don't
understand the source of the errors. They include:

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1673, <GEN0> line 25.

Use of uninitialized value in addition (+) at /usr/lib/perl5/site_perl/
5.8.8/Bio/Align/DNAStatistics.pm line 1505, <GEN0> line 25.

Use of uninitialized value in subtraction (-) at /usr/lib/perl5/
site_perl/5.8.8/Bio/Align/DNAStatistics.pm line 1506, <GEN0> line 25.

My alignment object has gaps, but I believe this module handles gaps.
The data I am analyzing comes from recently diverged species, so I
wonder if the errors could originate from a lack of substitutions.

Any help would be much appreciated.

Thanks!
Sarah.Kingan at rochester.edu


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