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

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