PyCogent: a toolkit for making sense from sequence

Table 1 Summary of features of selected comparative genomics tools

Feature	PyCogent	HyPHY	P4	BioPython	Mesquite	ARB	CIPRES^a
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.

ISSN: 1474-760X