Explore your trees directly in the browser, and annotate them with various types of data.

iTOL can easily visualize trees with 50'000 or more leaves. With advanced search capabilities and display of unrooted, circular and regular cladograms or phylograms, exploring and navigating trees of any size is simple.

https://itol.embl.de/

Address of the bookmark: https://itol.embl.de/

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

Address of the bookmark: http://christophergandrud.github.io/d3Network/

Address of the bookmark: https://www.onezoom.org/

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

The standalone version (Linux-based command-line) of RNAcon is freely available for the global scientific community.

Reference: Panwar, B.; Arora, A. and Raghava, G.P.S. (2014) Prediction and classification of ncRNAs using structural informationBMC Genomics 2014, 15:127

Address of the bookmark: http://crdd.osdd.net/raghava/rnacon/

Address of the bookmark: https://github.com/dutilh/CAT

CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes , including Maximum Likelihood or Bayesian tree inference, alignment trimming and evolutionary model testing. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions.

More at http://phylomedb.org/

db2db allows for conversions of identifiers from one database to other database identifiers or annotations. To use db2db select the input type of your data, changing the input type automatically changes the output options to the ones specific for the input selected. Then select one or more output types and add your identifiers in the ID list box. Set the remove duplicate values to 'No' if you do not want duplicates to be removed. Clicking on submit then returns a table of your inputs matched against all the outputs selected in the exact order as entered. Results can be limited to a particular taxon by entering it's Taxon ID. The performance will vary widely depending on the number of outputs and the options selected. Conversions to a single output with the default options should complete in a few seconds

Address of the bookmark: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php