Task list

Priority:

• make PDB-ID and Pfam-ID case-insensitive

• exclude hydrogen atoms from analysis (if present)

• refine README.md

• optimize help messages

• add general description to all scripts

• add date and author to scripts

• check which license to use

Optional:

• incorporate automatic generation of reference alignment into pipeline (see branch 'combine').

• add UniProt positions of reference Structure

• automatic PYMOL-file for contact visualization

• automate retrieval of SIFTS-file and PDB-files from internet

• write stdout of runall.sh to file

• check software for R as well

• write extensive documentation