List of applications executed via Biopython.

(under construction)

Python libraries

NumPy (Bio.PDB, Bio.Cluster, …)

Reportlab (Bio.Graphics only)

Matplotlib (Bio.Phylo.draw and draw_graphviz only)

RDFLib (Bio.Phylo.CDAOIO only)

NetworkX (Bio.Phylo.to_networkx and draw_graphviz only)

PyGraphviz or Pydot (Bio.Phylo.draw_graphviz only)

Applications

Bio.Align:

• Clustal Omega
• Clustal W
• DIALIGN
• MSAProbs
• MAFFT
• MUSCLE
• PRANK
• ProbCons
• T-Coffee

Bio.Blast

• NCBI BLAST+

Bio.Emboss:

• EMBOSS

Bio.PDB:

• DSSP
• NACCESS
• PSEA

Bio.Phylo:

• FastTree
• PhyML
• RAxML
• PAML (baseml, codeml, yn00)