About ODEN Format Tree Files

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In the case of ODEN format tree files, lines beginning with '>' are regarded as comments. The comment lines can be placed at the top or the end of the file. Lines beginning with 'O' (alphabet; not zero) are important. The program will search for 'tab' code on the line, and the text after the 'tab' is assumed to be the OTU name. Be sure not to remove the 'tab', otherwise the program can not read the tree file correctly. The OTU names must be written on consecutive lines. The length of OTU names should not be more than 255 characters.

To prepare an ODEN format tree file from DNA sequences, you need to use the ODEN system (developed by Dr. Y. Ina), which is a program package for molecular evolutionary analyses and is available on 'supernig' of National Institute of Genetics. First, start the ODEN system. Conduct the 'treenj' or 'treeupg' of ODEN with the '-g' option. The '-g' option is important; DendroMaker does not work without this option. Save the output into a file using redirection (>). Send the output file to your personal computer by ftp. Be sure to use ftp to send the data file because the data file contains 'tab' in it.


supernig% oden
supernig% distn sequence.dat | dmatn | treenj -g > NJ.TRE
supernig% distn sequence.dat | dmatn | treeupg -g > UPG.TRE
supernig% exit
supernig% ftp (IP address of your personal computer)
ftp> mput NJ.TRE
ftp> mput UPG.TRE
ftp> quit
supernig%