Wishlist or Issues

Fix Sequence vs. pdb numbering issue:

• add a tool to extract FASTA sequence from PDB file
• add feature to provide uniprot id to download FASTA sequence file
• extract residue numbers from prmtop

In dyno_aln_analysis:

• Per column amino acid frequencies
• Pairwise aminoacid frequencies for any two or list of any two positions
• Cummulative coevolution scores

dyno_pwie:

• make it clear that prmtop is the only supported format
• improve help message

dyno_2_dmatrix:

• add filter function to calculate J-efficiency score per geometric vector

dyno_3_jmatrix:

• remove Full scan message on -l
• elaborate on scaling s value

dyno_4_networks:

• improve example message
• use j-eff score to filter J_Vec values, to add a message to the user when network analysis might not be meaningful