Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for January, 2014

    How to cite PHYLIP

    10th January 2014

    Official PHYLIP FAQ does suggest a few ways to cite the software, but I believe that the best citation is mentioned in the wikipedia PHYLIP article: pubmed reference for PMID 7288891. This PubMed citations seems the best, because

    • it does mention the software tool implementing the maximum likelihood approach,
    • it is likely the earliest mention of the PHYLIP software (which was distributed since around 1980),
    • it refers to a journal indexed by pubmed, and
    • according to Google Scholar, it was already cited over 6660 times :)
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    Debian command of the day: popcon-largest-unused

    2nd January 2014

    From the Debian squeeze to wheezy upgrade guide:

    Remove packages that take up too much space and are not currently needed (you can always reinstall them after the upgrade). If you have popularity-contest installed, you can use sudo popcon-largest-unused to list the packages you do not use that occupy the most space. You can find the packages that just take up the most disk space with dpigs (available in the debian-goodies package) or with wajig (running wajig size). They can also be found with aptitude. Start aptitude in “visual mode”, select Views → New Flat Package List, press l and enter ~i, then press S and enter ~installsize. This will give you a handy list to work with.

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