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  • News & Commentary - Message forums

    Software: BIRCH - Release 2.2
    Submitted by Brian Fristensky; posted on Wednesday, May 23, 2007

    Submitter

    CHANGES

    • Fixed an error in birchconfig.sh which failed to detect when python was absent from the $PATH.
    • NCBI has split the GenBank ACCESSION index among several files. gbupdate has been revised to automatically downoad and install all of these files.
    • Taverna has been upgraded to version 1.5.1.
    • The Network Entrez client no longer works, and has not been supported by NCBI for some time. It has been removed from BIRCH.
    • NCBI Sequin has been upgraded to version 7.3.
    • The Phylip TREEDIST program has been added to tGDE.
    • In GDE, if FEATURES is launched with no sequences selected, getob would go into an infinite loop. This has been fixed in FEATURES.
    • MrBayes 3.1 has been added to BIRCH. MrBayes uses Bayesian methods for phylogenetic analysis of nucleic acids, proteins, molecular marker and discrete morphology data.
    • On some linux-intel systems, sequin would not run because it could not find two library files (libXm.so.2,libXp.so.6). Sequin is now run through a wrapper script that adds this file to the LD_LIBRARY_PATH.
    • The Phylip PARS program has been added to mGDE
    • Bluejay has been updated to version 0.701
    BIRCH can be downloaded from the project home page at: home.cc.umanitoba.ca/~psgendb

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