Tag Archives: phylogenetics

SNPpets_2

Friday SNPpets

This week’s SNPpets include items just posted to bioRxiv–which is lately where I see all the really intriguing tools. Including the awesomely-named “Clusterflock”. In a popular related item, someone responds to the Biostar question, “why are there errors in bioinformatics software?”. We have bat and bean genomics. And conch and lobster DNA. There’s at least 2 efforts to coordinate/wrangle human public genomes. And more.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • RT @32nm: ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature — Bioinformatics http://ff.im/x9hQ2 Hat tip to Mitsuteru Nakao [Mary]
  • The beginning of population level structural variation information on the human genome, from the at the  1000 genomes project. Hat tip to GenomeWeb [Jennifer]
  • Registration for the March 2011 GMOD Meeting is now open. See the wiki page at March 2011 Community Meeting. [Mary]
  • Need to assemble and analyze large datasets for multigene phylogenetic analysis? Might want to try out the new iPhy. Paper here. [Trey]
  • Ok, I had to go look at this–not what I expected…. : Top 200 Genomic Females list for Feb. 2011 is NOW ONLINE at http://bit.ly/i0Nj3O via @holstein_world. Yes, the name did clue me in, but I still had to look. [Mary]
  • Scientific Reports: interesting new venture by Nature Publishing Group. [Jennifer]
  • I love when rare diseases can shine lights into the darkness–very neat story on arterial calcification. Fascinating: RT @NatureNews: Solution to medical mystery offers treatment hope http://ff.im/-xiZYE [Mary]

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • NWChem for High-Performance Computational Chemistry has recently gone Open Source. (HT GenomeWeb) [Jennifer]
  • DIYGenomics relates an iPhone app that compares consumer genomics collections. [Mary]
  • A poster on BridgeDB, a resource for ID conversions. Hat tip to Chris Evelo. [Mary]
  • Sanger has done a very nice site for personal genomics and general background on the human genome, aimed largely at the general public and at teachers. http://www.yourgenome.org/ [Mary]
  • Nice phylogenetic analysis site for building protein phylogenies and structure predictions: PhyloBuilder [Trey]
  • Wired magazine had a fun take on some metagenomics from the Galaxy team. [Mary]
  • Via tweet: RT @dgmacarthur: 50% of UK respondents would take free genetic testing, but only 5% interested at current DTC prices: http://bit.ly/b7tDvx [Mary]
  • I completely missed World Statistics Day. No fireworks. No cake. Nuthin’. Sigh. [Mary]

Tip of the Week: PhyloWidget

Got phylogeny? So, you’ve created a phylogeny using some software and would like to draw the tree from the Newick formatted file* you exported. Of course there is no shortage of tree drawing programs out there (or phylogeny generating ones either). We found another one recently; a web-based, API-usable, opensource tree drawing tool that is quite intuitive and functional. It’s called PhyloWidget. The paper describing PhyloWidget is here and you can find some very nicely done step-by-step instructions here. I’ve done a quick 4 minute tutorial here to give you a quick overview. If it looks like something you could use, you might want to delve into it right away, or check out their ‘walk through.’ Happy climbing.

*Here’s the file I use in the tip: ((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);

Open Access Evolution

Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open access’ and ‘free online access’ journals) and is asking if anyone knows of any others. He hasn’t asked for it yet, but I’ve got some ideas for open source/access phylogeny analysis programs and/or databases. I’ll post a few of those in the coming week or so, but for now here is a link to a list of such programs (some on this list I’m not sure are open source, I’ll cull these later too).