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Table 5 Summary of representative software related to analysis applicable to tree visualization.

From: A reference guide for tree analysis and 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
  1. The table is not a complete summary but an overview of the features related and mentioned to the main text as well as their connectivity. Last Yes* for clustering refers to distance matrix based phylogenetic tree construction methods such as NJ and UPGMA.