BioShell functionality

File formats handled

PDB, FASTA, CIF, ALN, XML (most notably these produced by blast+), SS2 (PsiPred output), CHK (legacy blast profiles) MAT (PSSM files produced by PsiBlast)

Sequence processing

sequence sorting, filtering, conversions between formats

Structure processing

substructure extraction

Structure calculations

distances, angles, dihedral angles, contacts, hydrogen bonds, superimpositions (Kabsh algorithm), crmsd, GDT, tm-score

Statistical & numerical analysis

hierarchical agglomerative clustering, spline approximation, kernel density estimation, expectation-maximization