Function reference • agvgd

Align-GVGD main function

agvgd(): Align-GVGD (A-GVGD)

Protein sequence alignment

alignment_file(): Pre-bundled alignments

read_alignment(): Read a protein sequence multiple alignment

res_to_poi(): Convert a residue position to an alignment position

poi_to_res(): Convert an alignment position to residue position

Utility functions

amino_acids(): The 20 standard amino acids

read_substitutions(): Read a file with amino acid substitutions

write_alignment(): Export an alignment to FASTA

write_substitutions(): Generate and export a list of substitutions

profile_to_alignment(): Converts a sequence profile to an alignment

Align-GVGD low-level functions

cpv_ranges(): Determine CPV ranges

gv(): Grantham variation

gd(): Grantham deviation

dev(): Deviation function