I got a chance to benchmark my problem (650 columns * sequences) and model the length of time the calculation took to perform a basic PCA on a windows 11 computer. As the calculation is not CPU intensive the length of time to take the calculation is probably informative.
Time in seconds = 1.47668496473e-8 * sequences ^ 3.08800867902526
So time is proportional to the cube of the number of sequences. This table gives an idea how this plays out.
| Time | Sequences | ||
|---|---|---|---|
| 1 minute | 1300 | ||
| 1 hour | 4900 | ||
| 1/2 day | 10900 | ||
| 1 days | 13600 | ||
| 1 week | 25600 | ||
| 2 weeks | 32000 | ||
| 1 month (30 days) | 41000 | ||
| 2 months (60 days) | 51,300 |
In terms of memory for 30,000 sequences (the largest PCA tried) the calculation used up to 27GB but about a week into the calculation it used for a relatively short amount of time 38GB which would result in an out of memory error for 32GB machines.
So summing up, the limit to PCA size of calculation with Jalview is time (predictable) and peak memory usage (not easy to predict) .