Evolution Tree

Deutsche Version

The evolution tree shows putative pathways of karyotype development during tumour progression.

All suggested pathways ought to be regarded "putative" because only mulitple analysis of a patient's karyotpe over a long period of time can provide a good basis for a "real" pathway. Here, the evolution steps have to be reconstructed from data of many patients at different stages fo tumour progression.

Not always is the first rearrangement to become cytogenetically visible also the start event of a tumour progression. It could be a later event which will then start its typical evolution pathway. Also such cases are meant to become detectable.

Enter the file containing the data and its data format, the style of data pre-processing, the maximum number of cases to be analysed, the number of rearrangements to be displayed, and further parameters.

Possible data formats are the format of the Mitelman database, or a very simple custom format just containing a case identifier and the karyotype spearated from it by a tabulator or other separator per line; that format is also used for CGH data. For more information, see the "HowTo on Data Formats."
If you are not familiar with getting data from the Mitelman database, please have a look at the HowTo "Retrieving data from the Mitelman database". Please note that some data in the Mitelman database do use an older version of the ISCN. Such data may still be compatible with ISCN 1995 and then be analysed correctly, but some data may be no more compatible and thus not be parsed correctly.

Data can be processed "as is", or they can be translated into the SCCN or into Cytoband data; here, you can also select the virtual banding resolution of the processed data.

For more info on the Evolution Tree, you may also have a look at the description of its desk top version and the calculation of the data.




 Mitelman    Custom Format (Banding Analysis)   Custom Format (CGH)

For Custom Format Only:

Separator:  Tabulator   Pipe ("|")   Blank (" ")

Data Processing:

Use data

as is

or process to

   SCCN    Cytoband List

at a resolution of

2 Digits    1 Digit   Chromosomal Arm

Number of cases:

The maximum number of cases is limited for technical reasons (duration of calculation) to the default value given below. You may use an even lower value.

Note that useful results can hardly be obtained with less than 100 cases.

Maximum Cases:
Total Cases:
Valid Cases:

Other drawing parameters:

First Event Frequency:
Frequency Decrease Factor:
Minimum Event Count:
Binning Threshold:
Dependence Threshold:
Maximum Depth:


Citation of the CyDAS Package

To cite the use of the CyDAS Package from this Website in a publication, please quote the following:
Hiller B, Bradtke J, Balz H and Rieder H (2004): "CyDAS Online Analysis Site", http://www.cydas.org/OnlineAnalysis/

To cite the use of a program of the CyDAS package (a program of the package or a program of your own linking a program of the package) in a publication, please quote the following:
Hiller B, Bradtke J, Balz H and Rieder H (2004):
"CyDAS: a cytogenetic data analysis system",
BioInformatics 2005 21(7):1282-1283; doi:10.1093/bioinformatics/bti146.
Bioinformatics Advance Access originally published online on November 16, 2004 [Abstract] [PDF] [HTML-Text]

Please send your comments and inquiries to: info@cydas.org