- *.afa - aligned fasta - these are the alignments of the sequences
you have uploaded. Read here how to view them.
- *.png files: 1D score maps
- *.pml - Pymol script, used to produce *.pse, pymol session file.
Read here about how Cube presents results mapped on a structure,
or here about Pymol in general.
- nameindex - table of shortened names used by the server, side by side
with the original header files
- cmd - parameter file for either specs or hypercube
(downloadable code behind Cube server)
- *.score - output scores in plain text format; columns are separated by space
- *patched.afa and specs_out.patchlog - when possible, Cube treats missing residues
as being identical to what is seen in a taxonomically close species; *.patchlog
details which positions were treated in such way, and which species wer used as a template
- *stdout and *stderr - output from the used code; useful for diagnostics, but can otherwise be ignored