The MSA package for multiple alignment fails to write multiple alignments to file (PDF) because of memory limitations (save size and main memory size)

! TeX capacity exceeded, sorry [main memory size=1500000].

! TeX capacity exceeded, sorry [save size=15000].

I am trying to msaPrettyPrint 20 sequences of about ~1000 nucleotides each.  This shouldn't be so bad...

There are indeed limitations of the TeXshade package on which the function msaPrettyPrint() is based (see also Section 7.7 of the package vignette). However, I think that 20 sequences with ~1,000 bp each should not be a problem. If possible, please send me your sequences and the output of sessionInfo() on your system. Please send the data privately to msa@bioinf.jku.at. If there is anything secret about the sequences, you can anonymize the names. Ok?

Best regards,
Ulrich ('msa' package maintainer)