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Table 1 Comparison to other tools Itemized comparison of the features of Caryoscope ([15]), CGHAnalyzer ([12],[22]) and SeeCGH ([11],[23]).

From: Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

  Caryoscope CGHAnalyzer SeeGH
Platform Java (runs on any popular platform) Java (runs on any popular platform) Microsoft Windows
Application availability Unlimited use; no signup Unlimited use with signup Free with signup for academics
Installation process Install Java; run application directly from Web Install Java; install application Install MySQL; install application; configure database tables
Input file formats Single input file; spreadsheet compatible text or General Feature Format (GFF) Multi-component input; text-based input formats Text-based input formats
Internal data format Text file Text file or database MySQL database
Source code availability Free download Download with signup Not available
Source code license Open Source Unknown N/A
Internal code dependencies All Open Source Depends on some commercial software N/A
Superimposed karyotype plot No Yes Yes
Informational summary for each feature Yes, configurable in application settings Yes, fixed tabular format Yes, fixed tabular format
Web link from each feature Yes, configurable in application settings Yes, fixed Ensembl or GoldenPath links No
Data points in genome coordinates Yes Yes Yes
Data points in linear order No Yes No
Simultaneous display of multiple experiments No Yes No
Zoomable display Yes No Yes
Part of a more complete analysis framework No Yes (TIGR MeV) No
Built-in data point filtering No No Yes
Whole-genome view Linear chromosomes Concentric circles representing chromosomes Linear chromosomes
Generate graphics from command line Yes No No