||Task||Name||Licence||Packaging||Importance||Listed on microbio.wml?||
||Hapoltyping||[[http://www.biostat.umn.edu/~nali/SoftwareListing.html|Hotspotter]]||no licence||did not build out of the box on ppc|| ||no||
||Association studies||[[http://claire.bardel.free.fr/software.html|altree]]||as Perl itself||unofficial ([[http://dept-info.labri.fr/~danjean/deb.html#altree|ens-lyon]])||free||no||
||Linkage desequilibrium studies||[[http://www.genome.mcgill.ca/~mlemire/software.html|SUP]]||GPL||Depends on FastSLINK||free||no||
||QTL / SNP analysis||[[http://www.well.ox.ac.uk/happy/happyR.shtml|happy]]||[[http://www.well.ox.ac.uk/happy/disclaimer.shtml|free]]||R package||free||no||
||QTL analysis|| R/qtl||free||Debian R package r-cran-qtl||important||?||
||QTL analysis||[[http://statgen.ncsu.edu/eQTLViewer/|eQTLViewer]]||GPL||depends on perl||free||no||
||Association analysis||[[http://pngu.mgh.harvard.edu/~purcell/plink|PLINK]]||GPL||Looks simple||free||no||
||Haplotype analysis||[[http://www.broad.mit.edu/mpg/haploview|Haploview]]||MIT||depends on java||free||no||
||Analysis of recombination histories||[[http://www.stats.ox.ac.uk/~lyngsoe/beagle/|Beagle]]||LGPL||depends on C and python||free||no||
||Detection of microsatellites||[[http://code.google.com/p/msatcommander/|Msatcommander]]||GPL||Depense on wxpython, biopython, primer3||free||no||
||Linkage disequilibrium mapping||http://www.daimi.au.dk/~mailund/HapCluster/ HapCluster++||GPL||rpms available||free, up-to-date||no||
||Task||Name||Licence||Packaging||Importance||Listed on microbio.wml?||

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