BOL

Thanks for such an informative blog. I notice MCScan is missing. MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. More at...

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r2cat (related reference based contig arrangement tool) can be used to order a set of contigs with respect to a single reference genome. This is done by mapping the contigs onto the reference using a q-gram filter. The mapping is visualized in a...

Metagenomics: tools, comparisons and many applications http://blogs.biomedcentral.com/bmcseriesblog/2014/04/10/metagenomics-tools-comparisons-and-many-applications/

Squid – a simple bioinformatics grid http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1190159/?tool=pubmed

NetWorkSpaces for R http://nws-r.sourceforge.net/

R/parallel – speeding up bioinformatics analysis with R http://www.biomedcentral.com/1471-2105/9/390

R tutorial stuff at http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html

R for Bioinformatics http://www.evolution.unibas.ch/teaching/evol_genetics/1_Bioinformatics/lecture_notes/HS2013_9_R.pdf

APE: Analyses of Phylogenetics and Evolution in R language http://bioinformatics.oxfordjournals.org/content/20/2/289.abstract