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Table 1 Summary of features of selected comparative genomics tools

From: PyCogent: a toolkit for making sense from sequence

Feature PyCogent HyPHY P4 BioPython Mesquite ARB CIPRESa
Query remote database Yes No No Yes Yes Yes No
Control external Yes No No Yes Yes Yes Yes
Create novel substitution Yes Yes Yes No Yes No No
Novel sequence alignment Yes No No Yes No No No
Partition models Yes Yes No No No No No
Slice sequences Yes No No Yes No No No
Draw alignments Yes No No No No No No
Build phylogenetic trees Yes Yes Yes No Yes Yes Yes
Draw phylogenetic trees Yes Yes Yes No Yes Yes Yes
Visualization of model Yes Yes No No Yes No No
Parallel computation Yes Yes No Yes No No Yes
Customize parallelization Yes Yes No Yes No No Yes
Reconstruct ancestral Yes Yes No No Yes Yes Yes
Simulate sequences Yes Yes Yes No Yes No Yes
Graphical user interface No Yes No No Yes Yes Yes
Script based control Yes Yes Yes Yes Yes No Yes
Handle 3D structures Yes No No Yes Yes Yes No
Handling RNA secondary Yes No No No No Yes No
  1. PyCogent provides a unique combination of evolutionary modeling capabilities, visualization, and workflow control. Although many packages, including but not limited to those shown, provide some overlap in capabilities, PyCogent provides a combination of features that is uniquely suited to genome-scale analyses. aCIPRES requires purchase of commercially licensed software for core functionality. 3D, three-dimensional.