Miscellaneous software

The source code is also available from the Ubuntu archive. There is a variety of packages in bioconda, https://bioconda.github.io/recipes.html and conda-forge, https://conda-forge.org/feedstocks/.

We can trick the test even with compiling errors, e.g.,

sudo apt install loki
wget -qO- http://archive.ubuntu.com/ubuntu/pool/universe/l/loki/loki_2.4.7.4.orig.tar.gz | tar fvxz -
cd loki
# there are errors in compilng
cp /usr/bin/prep presrc
cp /usr/bin/loki lokisrc
cd test
# we are actually fine


This is according to https://www.decode.com/software/,

sudo `which conda` install allegro

Gudbjartsson DF, Thorvaldsson T, Kong A, Gunnarsson G, Ingolfsdottir A (2005). Allegro version 2. Nature Genetics 37:1015–1016


beast2-mcmc, beast2-mcmc-doc

It is Bayesian MCMC phylogenetic inference.

sudo apt install beast2-mcmc

It is the old merry fastlink 4.1P, https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html.

sudo apt install fastlink

loki, loki-doc

It implements MCMC method for linkage analysis. available from https://www.stat.washington.edu/thompson/Genepi/Loki.shtml

sudo apt install loki

See usr/share/doc/loki-doc/ for documentation.


This is according to http://csg.sph.umich.edu/abecasis/merlin/index.html,

sudo `which conda` install merlin


This is recently available,

sudo apt install plink1.9
plink1.9 --help --bfile


This is according to http://www.genetics.ucla.edu/software/,

sudo `which conda` install simwalk2