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    BIRCH Version 2.0
    Submitted by Brian Fristensky; posted on Thursday, October 05, 2006

    Submitter


    o Some Linux distributions (eg. Fedora) do not have Java, but rather,
    a GNU bytecode interpreter called gij. gij did not work correctly
    with ANY Java application tested. The solution is to install
    the real Java from Sun, and make sure that java (and not gij)
    is in the $PATH. Instructions for this workaround have been
    added to the Pre-installation instructions.
    o Fixed some problems with fasta2install.csh and fasta3install.csh.
    On some systems, these scripts did not correctly detect the
    available C-compilers.
    o A major re-organization and rewrite has been done for
    documentation linked from the BIRCH home page under
    the name "Using Unix from Anywhere". The new documentation
    goes into more depth on using commandline clients, VNC,
    X-terminals, and other thin clients.
    o The re-organization of documentation has prompted the addition
    of a new script (update-local.sh) to the update procedure used
    by birchconfig.java. During an update, files present in
    local-generic/public_html/remote, but not in local/public_html/remote,
    will be copied to local/public_html/remote. This will probably be expanded to
    encompass other files and directories in a later release.
    o Bluejay has been upgraded to the version dated Aug. 25, 2006.
    o local-generic/platform.source and platform.profile.source now contain
    code for setting BIRCH_PLATFORM automatically, using the Unix 'uname'
    command. This code is commented out, and must be uncommented to take
    effect. This feature is still being tested.
    o For distance phylogeny methods run by mGDE, restdist.csh failed to
    generate multiple datasets for resampling methods (ie. bootstrapping,
    jacknifing etc.) This problem only affected molecular marker
    distance methods, and not sequence distance methods. This
    problem has been fixed.
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