<html><div style='background-color:'><P>Hi</P>
<P>Currently i am a first time user of R Software.</P>
<P>I am trying to run a hierachical clustering of binding site similarities of some ligands.. I need to use Single Linkage. I am trying to run a command line version of the program. I already have a distance matrix of similarity scores available as a text file. The output of clusters needs to printed as a dendrogram. Can I choose the option to print the cluster results as a <STRONG>text file </STRONG>, as well as to <STRONG>view the tree as a PDF</STRONG>? Has anyone done something similar to this?</P>
<P>Any help will be great</P>
<P>Thanks!</P>
<P>Shalini<BR><BR></P><BR><BR><BR>
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From: <I>Titus Brown <titus@caltech.edu></I><BR>Reply-To: <I>titus@idyll.org,General discussions about software development in bioinformatics <biodevelopers@bioinformatics.org></I><BR>To: <I>ibtissem grissa <ibtissem.grissa@gmail.com></I><BR>CC: <I>General discussions about software development in bioinformatics <biodevelopers@bioinformatics.org>,titus@idyll.org</I><BR>Subject: <I>Re: [Biodevelopers] download bacterial genomes</I><BR>Date: <I>Mon, 19 Jun 2006 08:52:06 -0700</I><BR>>On Mon, Jun 19, 2006 at 05:45:22PM +0200, ibtissem grissa wrote:<BR>>-> ><BR>>-> >What about:<BR>>-> ><BR>>-> >ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria<BR>>-><BR>>-> yes, but I found only complete and published genomes there,<BR>>-> what I need is to have the maximum of genomes, even if they are not<BR>>-> completed or
public.<BR>>-><BR>>-> ? Or you could look at TIGR and JGI sites; JGI in particular may have a<BR>>-> >few that aren't anywhere else.<BR>>-><BR>>-><BR>>-> And I need to download them by an automatic way, so how could I check if<BR>>-> they don't exist elsewhere automatically.<BR>>-><BR>>-> Furthermore, I want to have all the information about genomes, and<BR>>-> especially the taxon classification of the organism<BR>>-> (Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;<BR>>-> Enterobacteriaceae)<BR>><BR>>I don't actually know of an electronic source for that information,<BR>>although it may be possible to retrieve it from NCBI taxonomy. I'm sure<BR>>if you browse around NCBI or TIGR you can find it.<BR>><BR>>Most microbial genomes get finished relatively quickly, because
they're<BR>>so *tiny* ;). I don't think there'll be much of a lag, so you might<BR>>want to just try out your algorithm on the already finished ones.<BR>><BR>>You can't get non-public ones ;).<BR>><BR>>In any case, if you do find a good source for all this information, please<BR>>repost it to this list (or send it to me personally ;). I'd be very<BR>>interested.<BR>><BR>>thanks,<BR>>--titus<BR>>_______________________________________________<BR>>Biodevelopers mailing list<BR>>Biodevelopers@bioinformatics.org<BR>>https://bioinformatics.org/mailman/listinfo/biodevelopers<BR></FONT></BLOCKQUOTE></div></html>