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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
...How to cite ADOMA:
Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083
http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
NGS compute distro proloaded with pipeline analysis software
Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission.
HOWTO:
1) Set VM network settings to a bridged adapter type.
2) Load VM to client
3) From host:
$ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure'
--- passwd = 616287xx
5) or ssh into host with X forwarding, and type runme
This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client.
...
parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS.
A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run.
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