I have trimmed and translated my NGS data and now have all the amino acid sequences in file: trans_seqs1 (Large AAStringSet, 14.7 Mb).
These have been quality controlled down from the original 600000 sequences.
Min. 1st Qu. Median Mean 3rd Qu. Max.
10.00 20.00 20.00 19.97 20.00 39.00
When I try aligning all the sequences (widths between 18-20) I get this error;
seqsalign <- AlignSeqs(trans_seqs1)
Determining distance matrix based on shared 3-mers:
| | 0%
Error: protect(): protection stack overflow
What can I do? Is it the function or my computer (Windows 7, 64bit operating system, 8GB RAM)?
I have also tried using the msaClustalW function but Clustal does not seem to align more than 500 sequences at a time. Can anyone suggest a package to align such a large amount of sequences in one go?