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1

Check out PGDSpider. The inputs and outputs table indicates that it supports conversion between FASTA and FSTAT formats, among many others.


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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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I wouldn't expect different methods to give the same results. Further, why are you even testing non-normalized datasets, the results of that are completely and utterly useless for any purpose other than showing that normalization is important. In addition, an T-test is a special case of an ANOVA (and of course limma is itself using a moderated T-test, though ...


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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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You can try this: BLAST each sequence to every other sequence (pairwise). Every alignment (with some defined cutoff) denotes a connection. Map all connections. If a sequence is connected to some other directly or indirectly, it falls in a group. Put all the sequences that seq1 aligns to, in Group-1, then go to the alignments of these sequences; put all ...


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Do you really need BLAST? That is, are the sequences different enough from each other that you need an algorithm that looks for large differences between them? Maybe you could use something like Phrap, which should put together contigs for you, if the sequences which should go together are very close to identical.


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I'm not clear what "Locus", "Main locus", and "IGMT group" mean here exactly. Specifically, what is the difference between "Locus" and "Main locus"? From the same site: A locus is a set of IG or TR genes that are ordered and are localized in a same chromosomal location, in a given species. […] A locus comprises the genes of different ...


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IMO irrespective of country and level (undergrad/Masters), if you can run a job on a High Performance Computing cluster or a supercomputer, you should mention that on your resume. And sure, you can use that in your statement, especially given the fact that not many have access to it, you had the rare opportunity and made full use of it. In my experience, I ...


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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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