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  • UpdateMega - Interleaved MEGA file management tool

    Sample FASTA | Sample SEQ | Sample Interleaved MEGA | GUI | Download (1.2 MB Zip File)
    Instructions

    UpdateMega is a Perl application originally developed to pipeline MLST at Dr. Tom Whittam's Laboratory. It automates the steps involved in incorporating new sequences into an interleaved mega file. The output interleaved mega file is ready for phylogeny analysis using MEGA2.

    It is assumed that input sequence files are trimmed sequences generated after allignment of consensus files, either in FASTA format (*.fas) or in SEQ format (*.seq). A FASTA file can contain more than one sequence. A SEQ file contain only one sequence. It is also assumed that each input sequence has a name following the naming system: 'strainName_locusName.seq'.

    For every input sequence, the tool checks sequence ambiguity and the length of the sequence before incorporating it into the output mega file. If the input sequence contains characters other than A/a, T/t, G/g, C/c and -, or the length of the sequence is not consistent with the length of sequences recorded in the input mega file, the sequence will not be incorporated.

    The zip file contains the window executable UpdateMega03.exe, the source code UpdateMega.pl and the README file.

    To use the tool, first load sequence files (*.fas and/or *.seq). It is recommended that to put all sequence files in one folder and use the load directory method. If your sequence files are distributed in different folders, you will have to run update seperately for each folder. Then select the interleaved meg file to be updated. If you are not interested in keeping a logfile in which all running status recorded, you can cancel the logfile check box. Click Update button will activate the update process. Running status will be shown in the window. Click Quit button will close the GUI.

    Contact stec@cvm.msu.edu
    Operated by Shannon D. Manning at Michigan State University