Table 5 Summary of representative software related to analysis applicable to tree visualization.
Software | Availability | Visualization | Interfaces | Tree Format | Clustering Analysis | Phylogenetic/Evolutionary Analysis | Microarray Analysis | Sequence Alignment Analysis |
|---|---|---|---|---|---|---|---|---|
MATLAB | Commercial | Yes | BioPerl, BioJava, C, Java, Perl | Newick | Yes | Yes | Yes | Yes |
MEGA | Free for use in research | Yes | PAUP, PHYLIP | Newick, Nexus | Yes* | Yes | No | Yes |
PHYLIP | Free | Limited | written in C | Newick | Yes* | Yes | No | No |
Geneious | Commercial; Free trial available | Yes | PAUP*, MrBayes, PHYLIP, MEGA | Newick, Nexus | Yes* | Yes | No | Yes |
PAUP* | From version 4.0 on must be purchased | Limited | PHYLIP, MEGA | Nexus | Yes* | Yes | No | No |
MrBayes | Free | Limited | written in C | Nexus | No | Yes | No | No |
HCE | Free for use in research | Yes | Does not apply; Output: tab delimited .txt or .bmp files. | Does not apply; Data Input: tab delimited .txt or .xls files. | Yes | No | Yes | No |
TM4 | Free for use in research | Yes | Does not apply; Output: tab delimited .txt or .tiff or .env, TM4 specific etc files. | Does not apply; Ability to save clusters and trees in Newick, Nexus. | Yes | No | Yes | No |