I have checked the calculation with alignment-free distances and it performs extremely fast. For 500 sequences on my computer it takes about 10 s versus about 4 minutes (=240 s) with the pairwise alignment, so about 25 x faster.
Also the results look roughly OK.
This is a big improvement to allow approximate calculation of distances for big data sets.
While doing this, I have noted a few small issues:
Of course, when using the Alfpy calculation, it is not possible to get alignments printed (the program basically crashes). So, when the user selects the Alignment-free option AND the "print alignments checkbox, an error message should appear saying "The Print alignments option cannot be selected with Alignment-free distance calculation".
Please in the GUI, change "TaxI2" to "TaxI3" so that we immediately see which program we are working with, even if the GUI will be changed later anyway...
When running the analysis and the progress of the analyses are shown in the left box, as first information it says "Distance calcution".
Please correct the typo and change to "Distance calculation"
I have checked the calculation with alignment-free distances and it performs extremely fast. For 500 sequences on my computer it takes about 10 s versus about 4 minutes (=240 s) with the pairwise alignment, so about 25 x faster.
Also the results look roughly OK.
This is a big improvement to allow approximate calculation of distances for big data sets.
While doing this, I have noted a few small issues:
Of course, when using the Alfpy calculation, it is not possible to get alignments printed (the program basically crashes). So, when the user selects the Alignment-free option AND the "print alignments checkbox, an error message should appear saying "The Print alignments option cannot be selected with Alignment-free distance calculation".
Please in the GUI, change "TaxI2" to "TaxI3" so that we immediately see which program we are working with, even if the GUI will be changed later anyway...
When running the analysis and the progress of the analyses are shown in the left box, as first information it says "Distance calcution". Please correct the typo and change to "Distance calculation"