<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38055?offset=120 https://bioinformaticsonline.com/bookmarks/view/32134/lifemap Mon, 10 Apr 2017 05:42:37 -0500 https://bioinformaticsonline.com/bookmarks/view/32134/lifemap <![CDATA[Lifemap]]> Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning.

 The current tree contains ALL species present in NCBI taxonomy as of October 18th, 2016: 1,135,169 species including 10,545 Archaea, 418,777 Bacteria and 705,847 Eukaryotes. The Lifemap tree is updated every two weeks.

 All the nodes in the tree are clickable. This displays various information and options:

  • The species name (and the associated common name if there is one)
  • The rank (kingdom, family, class, species...)
  • Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)
  • Possibility to download the corresponding subtree in newick extended format
  • Possibilty to get the whole lineage from the current node/tip to the root of the tree.

Address of the bookmark: http://lifemap-ncbi.univ-lyon1.fr/

]]> Jit https://bioinformaticsonline.com/opportunity/view/41899/stay-at-home-revbayes-workshop Sat, 20 Jun 2020 11:53:24 -0500 <![CDATA[Stay-at-Home RevBayes Workshop]]> Stay-at-Home RevBayes Workshop
Location: Anywhere (online-only event)
Dates: 7/13, 2020 to 8/12, 2020
Instructors: Joëlle Barido-Sottani, Walker Pett, Josh Justison, Wade Dismukes, Luiza Fabreti, Tracy Heath, Jeremy M. Brown, Rosana Zenil-Ferguson
Register: https://iastate.qualtrics.com/jfe/form/SV_02sCYRWbxYK9I5D

Description
This free online-only RevBayes workshop will provide an introduction to the theory and use of RevBayes, with a focus on (1) tree inference from molecular data, (2) analyses combining fossil and extant taxa, and (3) evaluating MCMC performance, with advanced topics including assessing model adequacy and macroevolutionary analyses. Additional topics may be added depending on the interests of selected participants. The format will be a combination of interactive video sessions (via Zoom or similar tools), real-time discussions over Slack, self-guided tutorials, and pre-recorded videos.

The initial session will resolve technical issues and present the basics of using RevBayes. Participants will then be expected to work through several tutorials on their own schedule, with the help of pre-recorded materials. A Slack forum will be open for questions and issues. The workshop will conclude with several online Q&A sessions with the instructors. The dates for the interactive sessions are currently tentative and may be adjusted depending on the schedules of the participants and instructors.

We are hoping to identify up to 15 participants for this online course. While we hope we are able to accommodate everyone who applies, we realize that this may not be possible because of time-zones and availability. If the number of applicants exceeds our capacity, we hope to organize a second round of sessions later in the year. Participants will not be charged for the course, but we will request that they commit to completing the tutorials and attending a majority of interactive sessions.

To apply to this course, please go to the registration form and submit your application by July 6, 2020.

More at https://revbayes.github.io/workshops/online2020.html

]]> https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data Fri, 07 Feb 2020 14:08:31 -0600 https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data <![CDATA[Free Genomics data !]]> The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction Mon, 08 Apr 2024 06:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction <![CDATA[MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction]]> MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

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