Table 1

Summary of features of selected comparative genomics tools
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

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.

Knight et al. Genome Biology 2007 8:R171   doi:10.1186/gb-2007-8-8-r171