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The PRANK and PAGAN algorithms have both come out of the Loytynoja lab in Finnland, and are stirring up the pot a bit. They use inferred phylogenetic relationships as a parameter, and tend to yield a much more 'gappy' alignment, supposedly due to more accurate handling of indels. For easy alignments the method doesn't matter so much, but if the sequences are ...


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You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll ...


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There are couple of them. First if you want to sequence analysis basic packages are : http://www.bioconductor.org/help/workflows/high-throughput-sequencing/ Also, Maqweb seems promising. http://maqweb.sourceforge.net


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None of them is integrase: P12497 Protein Gag-Pol polyprotein Gene gag-pol Organism Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1) P14350 Protein Pro-Pol polyprotein Gene pol Organism Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus) Even if you meant the integrase product of the polyprotein, the ...



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