Re: module Bio::TreeIO
Andreas Leimbach <[email protected]> Tue, 10 May 2016 20:21:41 +0200
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
just realized I didn't reply to list earlier, so here are my two cents. well, if you're willing to go outside Perl, there are plenty of options to cluster distances. E.g. R's `hclust` function with many hierarchical clustering algorithms (complete, average etc.) https://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html For examples with dendrograms (and package `ape`) see: https://rstudio-pubs-static.s3.amazonaws.com/1876_df0bf890dd54461f98719b461d987c3d.html Use the R package `amap` for parallellization: https://cran.r-project.org/web/packages/amap/index.html BioPython has also most of the distance/clustering functions of R implemented: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc234 Nice Python examples, I think, are integrated in pyani from Leighton Pritchard: https://github.com/widdowquinn/pyani I'm sure there are also Perl packages for clustering out there, just don't know about them. HTH, Andreas -- Andreas Leimbach Universität Münster Institut für Hygiene Mendelstr. 7 D-48149 Münster Germany Tel.: +49 (0)551 39 33843 E-Mail: [email protected] On 10.05.2016 20:08, Fields, Christopher J wrote: > On May 10, 2016, at 10:51 AM, Youensclark, Ken - (kyclark) <[email protected]> wrote: >> >> On May 10, 2016, at 5:54 AM, lskatz <[email protected]> wrote: >>> >>> That's what I thought originally too but the R package made it look like >>> there might be some magic bootstrapping going on with distances alone. If >>> there truly is no distance-matrix bootstrapping algorithm then I am left to >>> my devices and at least I can make use of assess_bootstrap(). >> >> I'm following this thread with interest not because I have anything to add about the Perl but because I've been using MinHash in an all-vs-all sample comparison application that runs on the stampede cluster at TACC: >> >> https://github.com/hurwitzlab/stampede-mash >> >> I'd love to know what all you're doing with a distance matrix as far as analysis and visualization. >> >> Ken > > Nice, we’ve been looking into mash as well for the same reasons. Nothing to report yet unfortunately (we haven’t even started). > > chris > > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l