Dear All,
I think it would be useful to add a %s or %f (containing megan sample filename) option to the existing %t and %i options. Such a function would be especially useful for e.g. a long reads / contigs export from a comparison with hundreds of samples.
In the current versions, you can do this without any distinction when exporting long reads / contigs, and the result will be a large collection of fasta files with no originated sample names.
Bests: Blaize