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very simple statistic, but I'm not sure how/where! (Read 4098 times)

rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	very simple statistic, but I'm not sure how/where! Oct 28^th, 2011 at 2:09pm I need to provide a colleague with the maximum % nucleotide and amino acid diversity in my set of sequences (overall and within subpopulations). everywhere I look I see mean measures! and I feel goofy for not being able to find this! thanks in advance, Rachel
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: very simple statistic, but I'm not sure how/where! Reply #1 - Oct 31^st, 2011 at 7:22am Hi Rachel, F_ST (a standard under Compartmentalization) is probably your best bet. This will compute mean pairwise diversity (no phylogenetic correction). Sergei
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rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	Re: very simple statistic, but I'm not sure how/where! Reply #2 - Nov 1^st, 2011 at 2:27pm thanks, Sergei. I'm after maximum measures of diversity, not mean, in order to compare to past published data. at this point I'm considering just a crude pairwise matrix, but the number of taxa involved makes me cringe with sore eyes just to imagine it. I'll keep looking. Rachel
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: very simple statistic, but I'm not sure how/where! Reply #3 - Nov 1^st, 2011 at 7:35pm Hi Rachel, If your sequences are aligned, I have a really fast command line utility that can compute pairwise TN93 distances on 50,000 sequences in <5 minutes and output the maximum as well as all distances above a fixed threshold. Let me know if you are interested. Sergei
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rbjmax YaBB Newbies Offline Feed your monkey! Posts: 17	Re: very simple statistic, but I'm not sure how/where! Reply #4 - Nov 2^nd, 2011 at 10:32am that would be super, Sergei! thank you! Rachel
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Sergei

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Re: very simple statistic, but I'm not sure how/where!
Reply #5 - Nov 3^rd, 2011 at 3:21pm

Hi Rachel,

Here you go. Do the usual Linux source install:

./configure
make
make install

You should now have the TN93dist binary which takes a .fasta file and a number of arguments (hopefully the help line is somewhat meaningful) and runs the pairwise distance calculation. Maximum distance is spooled to the console; only those distances exceeding the threshold you put on the command line are output to a file.

Sergei

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: very simple statistic, but I'm not sure how/where! Reply #6 - Nov 8^th, 2011 at 3:58pm Hi Rachel, A more documented version: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to Login Sergei
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