Tag Archives: phylogeny


Video Tip of the Week: iDigBio for access to historical specimens and more

idigbio_logoUsually for Thanksgiving week posting is light. In the past, we’ve all done turkey breeding and genomics, cranberry genome, and some people have included apples, potatoes, and more. But another key aspect of the holiday is to remember the past and thank those who came before. And as I was watching this video that crossed my desk, I was thinking about our really ancient ancestors and their companions on the planet. And those who have created and preserved specimens in museum collections documenting the planet’s history. Increasingly those things are being digitized when appropriate, and sometimes even sequenced now when possible.

Some people think of these types of things as “stamp collecting”. But I think we are going to find these resources increasingly valuable as more folks can access and explore them.

So I want to thank folks who have been collecting, curating, and documenting our planet and its species over the millennia. This week I highlight iDigBio and their specimen portal that will provide access to these important curated collections for researchers to take into the future.

This week’s video is only one of the presentations at their iDigBio Summit V. They have a great Vimeo channel with other talks, but this one on Digitized Data in Biodiversity Research caught my attention first. It talks about work in wrangling information in biodiversity, making it available for further work with tools and workflows. It’s a nice overview of the goals and umbrella of topics they are interested in. And also mentions PhyloJIVE, which can integrate phylogeny data and available specimens. That’s a very cool bridge, it seems to me.

iDigBio Summit V: Digitized Data in Biodiversity Research from iDigBio on Vimeo.

So as you are eating and drinking a diverse range of species over the next few days, thank evolution. And thank folks who have been monitoring biodiversity in the past, and moving the studies into the future, on this pale blue dot we share.

Quick links:

iDigBio Portal: https://www.idigbio.org/portal

PhyloJIVE: http://phylojive.acis.ufl.edu/PhyloJive


Nelson, G., Sweeney, P., Wallace, L., Rabeler, R., Allard, D., Brown, H., Carter, J., Denslow, M., Ellwood, E., Germain-Aubrey, C., Gilbert, E., Gillespie, E., Goertzen, L., Legler, B., Marchant, D., Marsico, T., Morris, A., Murrell, Z., Nazaire, M., Neefus, C., Oberreiter, S., Paul, D., Ruhfel, B., Sasek, T., Shaw, J., Soltis, P., Watson, K., Weeks, A., & Mast, A. (2015). Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi Applications in Plant Sciences, 3 (9) DOI: 10.3732/apps.1500065

Nelson, G., Paul, D., Riccardi, G., & Mast, A. (2012). Five task clusters that enable efficient and effective digitization of biological collections ZooKeys, 209, 19-45 DOI: 10.3897/zookeys.209.3135

Jolley-Rogers, G., Varghese, T., Harvey, P., dos Remedios, N., & Miller, J. (2014). PhyloJIVE: Integrating biodiversity data with the Tree of Life Bioinformatics, 30 (9), 1308-1309 DOI: 10.1093/bioinformatics/btu024


Friday SNPpets

This week’s SNPpets include a dinoflagellate genome; artificial base pairs in use; the relative joy of entrepreneurship graphed; hidden Galaxy features; free image resources from NIH; new and updated tools for various purposes–as always; a trait-matching challenge; and veterans who continue to do service by offering their DNA to researchers. Oddest thing: an ear built with van Gogh’s DNA. 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…

What’s the Answer? (phylogenetic tree tools)

reddit_iconThe previous What’s the Answer? post that we did on something at Reddit Bioinformatics was popular. It led people to some software they weren’t familiar with for editing multiple sequence alignments. So this week we’ll try another post from this subreddit that might be informative for folks interested in phylogenetic tree tools.

reddit question icon Suggestion for phylogenetic tree visualization tools

I’m an MS Biology student a bit more on the in silico side of things. One of the projects I’m involved in would require me to visualize (preferably) unrooted phylogenetic trees (based on miRNA sequences). I’m looking for suggestions regarding this problem, what tools should I use?

I’ve used FigTree and UGENE before but I’d like to broaden the palette of available tools.

–submitted by tronke

There were a number of popular tools in the replies: R tools ape, phytools and others, FigTree, Dendroscope, Mesquite, MEGA, and Archaeopteryx. Check out the full discussion thread over there.

Video Tip of the Week: JANE, comparing phylogenies

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When I was doing my Ph.D. in the ancient days of the Sanger Method sequencing and reading in the results with one hand on the keyboard and reading the GATCs on the read (and going to the lab in the snow uphill both ways), my purpose for slogging  through all that was to eventually get a phylogeny of the sequences of the retrotransposable elements I was studying. Why did I want that phylogeny? Because I was comparing the phylogeny of the retroelements to that of the species in which they reside. We were attempting to determine if these retroelements were stable within the taxa lineage (they are) or there was promiscuous horizontal transfer occurring. We did those comparisons, but it would have been nice to have a ‘cophylogeny reconstruction’ program :D. There are often times similar comparisons of phylogenies are necessary. Host-parasite studies, coevolution, etc. Jane is a software package (free with registration) that uses a heuristic approach, “running a genetic algorithm with an internal fitness function that is evaluated using a dynamic programming algorithm.” It can often give an optimal solution for that cophylogeny you are studying. Jane was developed in the research group of  Ran Libeskind-Hadas at Harvey Mudd College and you can  read more about the algorithm and approach here. They also have an extensive written tutorial. In these tips we usually focus on web-interface to tools, but I liked this package (and it’s free) and wanted to play around with it, so today I’ll walk you through a very quick intro to downloading and getting started with the tool. Quick Links: Jane Jane Tutorial CoPhylogeny Reconstruction TreeMap (another cophylogeny reconstruction software) CopyCat (yet another) Book Chapter on Cophylogeny and reconstruction Conow, C., Fielder, D., Ovadia, Y., & Libeskind-Hadas, R. (2010). Jane: a new tool for the cophylogeny reconstruction problem Algorithms for Molecular Biology, 5 (1) DOI: 10.1186/1748-7188-5-16

Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes)

ResearchBlogging.org Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December.

Oh, that’s not what this tip is about, it’s about database of orthologous groups of genes, eggNOG. We’ve mentioned eggNOG before several times, but only in passing or in relation (orthologous? :D) to another database or tool. Today, in perfect timing for the season, thought I’d do a quick tip to introduce eggNOG.

eggNOG is brought to you by the same research group that developed a lot of other excellent tools such as SMART (protein domains), STRING (protein-protein interactions, STITCH (protein-chemical interactions) , iTOL and so much more. Of course they do some fascinating research too.

eggNOG is a relatively straightforward database to use, but it has a wealth of information you might want to check out. As the recent paper in NAR states:

Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses…. Orthology, defined as homology via speciation, is a crucial concept in evolutionary biology and is essential for disciplines such as comparative genomics, metagenomics and phylogenomics. The concepts of orthology and paralogy, with the latter being defined as homology via duplication, have been used as a foundation to introduce the concept of clusters of orthologous groups: proteins that have evolved from a single ancestral sequence existing in the last common ancestor (LCA) of the species that are being compared, through a series of speciation and duplication events. Orthologous groups (OGs) have proven useful for functional analyses and the annotation of newly sequenced genomes  as orthologs tend to have equivalent functions.

eggNOG contains:

721 801 orthologous groups, encompassing a total of 4 396 591 genes…. from 1133 species.

For more about orthologous groups, methods used and pros and cons of methodology, you might want to check out the paper referenced below. They’ve included several informative and helpful reviews and references.

Right now, take a quick tour of what eggNOG can offer.

Quick Links:
STRING tutorial
SMART tutorial
Tip of the Week: iTOL

Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L., von Mering, C., & Bork, P. (2011). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges Nucleic Acids Research DOI: 10.1093/nar/gkr1060

Tip of the Week: Encyclopedia of Life

Today’s tip is going to diverge a bit from genomics today and revisit a tip I did two years ago on the Encyclopedia of Life, an ‘wiki-like’ encyclopedia of all know species. We I visited it then in the tip it was only about a year old. I had written about it a few months before and compared it to the The Tree of Life. The latter was focusing more on phylogeny and deeper branches, while the EOL focused on species pages (or leaves) and pulling all available data about all species. I also wrote about the iTOL last year too, an interactive Tree of Life phylogeny. With these and some other resources, there’s a wealth of taxanomic and phylogenetic data out there.

I’d like to see a bit more integration with EOL and TOL, but both projects seem progressed in the last two years. In today’s tip we are going to revisit EoL and reintroduce you to the site and visit the same places and see what has changed.

Tip of the Week: PhylomeDB

Gene phylogenies (as opposed to species phylogenies) can be very useful in determined gene function, history, orthology and paralogy predictions. PhylomeDB (link added!) is a database of gene phylogenies (or as they call them, Phylomes.. no end to the ‘omes is there? :). Currently there are over a dozen such phylomes from species like humans and yeast. The database allows you to obtain phylogenies of genes based on gene ID or BLAST, you can also get orthology predictions and alignments and more. Today’s tip is introducing you to the database.

Tip of the Week: uBIO federated taxonomic search

This week’s tip of the week introduces a thesaurus of biological names, called uBio.  http://www.ubio.org/ The uBio project aims to collect and organize biological names–historical and current–and make them available for searching or for use in other tools.  It also contains dozens of cool links to other tools and projects around taxonomy and biodiversity around the world. I found out about them from Trey’s recent Tip on the PhyloWidget tool–one of the links you can use after you build a phylogeny is to uBio.  This short movie focuses mostly on the basic search, and points to a few of the other related items.

A brief description of the project can be found at the project description at the Wood’s Hole Marine Biological Laboratory site:

The Main component of the uBio project is a Taxonomic Name Server that acts as a thesaurus. One Taxon can have many names and the same name can refer to many taxa; this project provides services to reconcile these differences. There are two component to this: NameBank, a repository of millions of recorded biological names, and ClassificationBank which stores multiple classifications and taxonomic concepts.

They collaborate with a huge range of projects, from natural history to biodiversity resources.  One of the available links included digitized access to the Nomenclator Zoologicus which is a descendant of Linnaeus’ Systema Naturae.

Check out uBio for some nifty taxonomic and biodiversity utilities. http://www.ubio.org

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);

Tip of the Week: Drawing a Tree

phylodendron_thumbSo, you’ve got your sequences aligned using Clustal, Muscle or T-Coffee (or other program), you’ve created a tree data file using PAUP, Phylip or one of the other many algorithms out there, now you want to draw and visualize those relationships. A good place to go to find a list of tools to do that is at the huge list of phylogeny tools at Department of Genome Sciences at the University of Washington (there is a lot more than just tree drawing of course!). Many of these tools are downloaded and feature rich, one might suit your needs, so check them out. One this tip points out is Phylodendron, which you can download, but also has a web interface. This will allow you to quickly draw a tree for viewing.