University of Glasgow

Roderic Page

![6e1f1693ed5d70b2f495e9a2c8666114 reasonably
small](http://lh3.ggpht.com/-HWLBZz22iF4/UH8So-uQThI/AAAAAAAACI4/JfXN8j5fSWo/6e1f1693ed5d70b2f495e9a2c8666114_reasonably_small.jpg?imgmax=800 "6e1f1693ed5d70b2f495e9a2c8666114_reasonably_small.jpg"){border="0"
width="100" height="100" style="float:right;"}James Rosindell\'s
[OneZoom](http://www.onezoom.org/) tree viewer is out and the paper
describing the viewer has been published in PLoS One (disclosure, I was
a reviewer):  
  

> Rosindell, J., & Harmon, L. J. (2012). OneZoom: A Fractal Explorer for
> the Tree of Life. PLoS Biology, 10(10), e1001406.
> doi:10.1371/journal.pbio.1001406.g004

Below is a video where James describes OneZoom.  
  

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OneZoom is fun, and is deservedly attracting a [a lot of
attention](https://twitter.com/search?q=OneZoom). But as visually
striking as it is, I confess I have reservations about fractal-based
viewers. For a start they make it hard to get a sense of the relative
size of taxonomic groups. Looking at the mammal tree shown in the video
above your eye is drawn to the monotremes, one of the smallest mammalian
lineages. That the greatest number of extant mammals are either rodents
or bats is not readily apparent. Fractal geometry also removes the
timescale, so you can\'t discover whether radiations in different clades
are the same age (unlike, say, if the tree was drawn in a
\"traditional\" fashion with a linear timescale). In some ways I think
fractal viewers are rather like the hyperbolic viewers that [attracted
attention about a decade
ago](http://graphics.stanford.edu/~munzner/h3/) - visually striking but
ultimately difficult to interpret. What I\'d like to see are studies
which evaluate how easily people can navigate different trees and
accomplish specific tasks (such as determining closest relationships,
relative clade diversity, etc.).  
  
![Hypviewer](http://lh6.ggpht.com/-1gvJTdI85ZA/UH8SqG0S79I/AAAAAAAACI8/ZIH9WfJz9MY/hypviewer.gif?imgmax=800 "hypviewer.gif"){border="0"
width="100" height="100" style="float:right;"}In some ways OneZoom
resembles Google Maps with its zoomable interface. But ironically this
only serves to illustrate a key different between OneZoom and Google
Maps. Part of the strength of the later is the consistent conventions
for drawing maps (e.g., north is up, south is down) which, when coupled
with agreed co-ordinates (latitude and longitude), enables people to
mash up geographic data. What I\'d like is the equivalent of
[CartoDB](http://developers.cartodb.com/examples.html) for trees.


James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One (disclosure, I was a reviewer):Below is a video where James describes OneZoom.OneZoom is fun, and is deservedly attracting a a lot of attention. But as visually striking as it is, I confess I have reservations about fractal-based viewers. For a start they make it hard to get a sense of the relative size of taxonomic groups.

OneZoom

Prompted by a conversation with Vince Smith at the recent [Online
Taxonomy](http://www.linnean.org/Meetings-and-Events/Events/Online+Taxonomy)
meeting at the Linnean Society in London I\'ve been revisiting
touch-based displays of large trees. There are a couple of really
impressive examples of what can be done.  
  

### Perceptive Pixel

  
I\'ve [blogged about this
before](http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html),
but came across another video that better captures the excitement of
touch-based navigation of a taxonomy. [Perceptive
Pixel\'s](http://www.perceptivepixel.com/) (recently [acquired by
Microsoft](http://venturebeat.com/2012/07/09/microsoft-buys-perceptive-pixel/))
Jeff Han demos browsing an animal classification. The underlying
visualisation is fairly sttaightforward, but the speed and ease with
which you can interact with it clearly makes it fun to use.  
  

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### DeepTree

  
  
DeepTree comes from [Life on
Earth](https://lifeonearth.seas.harvard.edu/) lab, and there\'s a paper
coming out by [@blockflorian](http://twitter.com/blockflorian) and
colleagues (I was reminded of this project by
[@treevisproject](http://twitter.com/treevisproject)):  
  

> Technique added: DeepTree (2012); Florian Block, Michael Horn, Brenda
> Phillips, Judy Diamond, Margaret Evans, Chia Shen
> [researchgate.net/publication/23...](http://t.co/cxwPnkC8 "http://www.researchgate.net/publication/230753646_The_DeepTree_Exhibit_Visualizing_the_Tree_of_Life_to_Facilitate/file/79e41503e4cfd0ea6a.pdf")
>
> --- treevis.net Project (@treevisproject) [September 21,
> 2012](https://twitter.com/treevisproject/status/249141462476939266){data-datetime="2012-09-21T13:42:08+00:00"}

  
  
For technical details on the layout algorithm see
<https://lifeonearth.seas.harvard.edu/downloads/DeepTree.pdf>. Below is
a video of it in use:  
  

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Both of these are really nice, but what I really want is to have this on
my iPad...  


Prompted by a conversation with Vince Smith at the recent Online Taxonomy meeting at the Linnean Society in London I've been revisiting touch-based displays of large trees. There are a couple of really impressive examples of what can be done.
<strong>
 Perceptive Pixel
</strong>
I've blogged about this before, but came across another video that better captures the excitement of touch-based navigation of a taxonomy.

Touching the tree of life

![34106 130
130](http://lh6.ggpht.com/-9ByM1xvgQdo/Tz1QEANkMLI/AAAAAAAABJE/XLFtQrzLAlU/34106_130_130.jpg?imgmax=800 "34106_130_130.jpg"){border="0"
width="130" height="130" style="float:right;"}The Encyclopedia of Life
have announced the [EOL Phylogenetic Tree
Challenge](http://eol.org/info/tree_challenge). The contest has two
purposes:  
  

>   
> It provides a testbed for the Evolutionary Informatics community to
> develop robust methods for producing, serving, and evaluating large,
> biologically meaningful trees that will be useful both to the research
> community and to broader audiences.  
>   
> It enables the Encyclopedia of Life to organise the information it
> aggregates according to phylogenetic relationships; in other words, it
> provides a direct pipeline from research results to practical use.  

  
  
First prize is a trip to [iEvoBio 2012](http://ievobio.org/), this year
in Ottawa, Canada. For more details visit the [challenge
website](http://eol.org/info/tree_challenge). There is also an [EOL
community devoted to this
challenge](http://eol.org/communities/98/newsfeed).  
  
Challenges are great things, especially ones with worthwhile tasks and
decent prizes. EOL badly needs a phylogenetic perspective, so this is a
welcome development.  
  
But (there\'s always a but), I can\'t help feeling that we need
something a little more radical. The tree of life isn\'t a tree. At deep
levels it\'s a forest, and even at shallow levels things are a
complicated tangle of gene trees. Sometimes the tree is clear, sometimes
not, and some of this is real and some reflects our ignorance.  
  
If you want a simple tree to navigate, then I\'d argue that the NCBI
tree is a pretty good start, and EOL already has this. What would be
really cool is to have a way to navigate that makes it clear that
phylogenetic knowledge has a degree of uncertainty, and that the \"tree
of life\" might be better depicted as a set of overlapping trees. The
mental image I have is of a collage of trees from different data sets,
superimposed over each other, with perhaps an underlying consensus to
help navigate. This visualisation could be zoomable, because in some
ways the tree of life is fractal. Trees don\'t stop at species, as the
wealth of barcoding and phylogeographic studies show. Given
computational constraints (not to mention visualisation issues), I
wonder whether there is an effective limit to the size of any one tree
in terms of number of taxa. What varies is the taxonomic scope. So we
could imagine a backbone tree based on slowly evolving genes, we zoom in
and more trees appear, but at lower levels, and finally we hit
populations and individuals, trees that may have 100\'s of samples, but
a very narrow scope.  
  
This is all rather poorly articulated, but I can\'t help wondering
whether a phylogenetic classification will end up distorting the very
thing we\'re trying to depict. It also looses connection with the
underlying data (and trees), which for me is a huge drawback of existing
classifications. There\'s no sense of why they are the way they are.
There\'s a chance here to bring together ideas that have been kicking
around in the phylogenetic community for a couple of decades and rethink
how we navigate the \"tree of life\".


The Encyclopedia of Life have announced the EOL Phylogenetic Tree Challenge. The contest has two purposes:First prize is a trip to iEvoBio 2012, this year in Ottawa, Canada. For more details visit the challenge website. There is also an EOL community devoted to this challenge.Challenges are great things, especially ones with worthwhile tasks and decent prizes.

EOL Phylogenetic Tree Challenge

Last week I was at the NSF \"Assembling, Visualising and Analysing the
Tree of Life\" Ideas Lab, run by
[KnowInnovation.com/](http://www.knowinnovation.com/). It was an
interesting experience, essentially a structured week of brainstorming
ideas.  
  
One thing I came away with is the feeling that our notions of the \"tree
of life\" are fuzzy, contradictory, and often probably unobtainable.
It\'s tempting to imagine all sorts of wonderful visualisations, and
loose sight of building something that is useful. Perhaps it\'s time
instead to think of \"Tree of Life version 0.1\".  
  
Imagine taking the NCBI taxonomy as a starting point. Yes it\'s
incomplete, and has almost no fossils, but it\'s freely available and
linked to a lot of data. Let\'s use a Google Maps-like viewer along the
lines I [explored earlier this
year](http://iphylo.blogspot.com/2011/03/zooming-large-tree-now-with-thumbnails.html).  
  
Then add annotation \"tracks\" to the tips. As a first pass these could
be taken from the [NCBI
LinkOut](http://www.ncbi.nlm.nih.gov/projects/linkout/) service, such as
the NCBI-Wikipedia mapping <http://iphylo.org/linkout>.  
  
![Ncbi
1](http://lh3.ggpht.com/-me96WuCex7s/Tll7STe0lrI/AAAAAAAAA-Y/T1Nqw-JZlYk/ncbi-1.png?imgmax=800 "ncbi-1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="410"}  
  
The NCBI tree is a classification rather than a phylogeny, so we could
add greater phylogenetic content by linking to phylogenetic databases,
such as [TreeBASE](http://www.treebase.org) and
[PhyLoTA](http://phylota.net). Imagine clicking on a node in the NCBI
taxonomy and seeing a display of all the phylogenies centred on that
node:  
  
![Ncbi
02](http://lh5.ggpht.com/-lAqpz4FgoEA/Tll7TUcuhpI/AAAAAAAAA-c/Hg3jDIdlSGw/ncbi-02.png?imgmax=800 "ncbi-02.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
  
Now we have a way to navigate a large tree, view annotations, and
display phylogenetic trees. All of this could be done fairly easily. The
key is to have services keyed by the NCBI tax_id used to identify nodes
on the tree.  
  
Among the next steps would be to add additional \"tracks\", perhaps
based on curated links analogous to the wiki-based NCBI-Wikipedia
mapping. For example, very basic habitat data (marine or terrestrial)
could be added, or geography, or host relationships (could be based in
part on the data already in GenBank).  
  
Given that the NCBI tree continues to grow, subsequent versions could be
released as the tree changes. Or we could \"fork\" the NCBI tree and
start to refine it based on phylogenetic information, and add taxa that
aren\'t in the genome databases (these taxa will need consistent
identifiers so we can map annotations on to them as well). Perhaps we
could use something like
[Git](http://en.wikipedia.org/wiki/Git_(software)) to manage this tree,
and to handle the necessary merging of updated versions of the NCBI
tree. People could edit the tree, or indeed fork it and come up with
their own.  
  
![Logo tmp reasonably
small](http://lh6.ggpht.com/-Lj8I4ebWeao/Tll7UA88ybI/AAAAAAAAA-g/cDWvJYHkz0c/logo_tmp_reasonably_small.png?imgmax=800 "logo_tmp_reasonably_small.png"){border="0"
width="128" height="128" style="float:right;"}There are lots of ways to
visualise trees (see [TreeVis.net](http://treevis.net) for some great
examples), but what I\'m after is a tool that is useful, that gives us a
sense of what we know and what we don\'t. I suspect that one of the
reasons we\'ve struggled with visualising the tree of life is that there
are lots of different notions about what it\'s for. In this case, I want
a tool to navigate data about organisms, one that we can easily add
annotations too.  
  
  


Last week I was at the NSF "Assembling, Visualising and Analysing the Tree of Life" Ideas Lab, run by KnowInnovation.com/. It was an interesting experience, essentially a structured week of brainstorming ideas.One thing I came away with is the feeling that our notions of the "tree of life" are fuzzy, contradictory, and often probably unobtainable.

Tree of Life 0.1 - annotating the NCBI taxonomy

Last night BBC One aired David Attenborough\'s [Charles Darwin and the
Tree of Life](http://www.bbc.co.uk/darwin/), which featured a lovely
\"fly through\" the tree of life:  
  

  
  
In conjunction with the TV show, the Wellcome Trust has launched the
[Interactive Tree of
Life](http://www.wellcometreeoflife.org/interactive/), a Flash-based
view of the tree of life. There\'s also a
[blog](http://wellcometreeoflife.blogspot.com/) about the project.
Here\'s a demo of the tree:  
  

  
  
The tree looks very nice, and a lot of work has gone into it, but I am
somewhat underwhelmed. The tree itself is tiny, and does a poor job of
conveying the relative diversity of life (e.g., no plants, bacteria, few
arthropods, etc.). It displays the tree on a 2D plane, and the user can
move relative to that plane. I\'m not convinced this is the best way to
display large trees. Something modelled on Perceptive Pixel\'s demo
might be more useful. I [blogged about
this](http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html)
last year, but the video host service has disappeared. You can see the
tree display 50 seconds in to the video below:  
  

  
  
There also seems to be some confusion over the license used. The
[disclaimer](http://www.wellcometreeoflife.org/about/disclaimer/) states
that it is [Creative Commons Attribution-Noncommercial 2.5
Generic](http://creativecommons.org/licenses/by-nc/2.5/), but the link
is to [Attribution-Noncommercial-No Derivative Works
3.0](http://creativecommons.org/licenses/by-nc-nd/3.0/). There\'s a
**big** difference. The disclaimer encourages us to remix it, the linked
license says that we cannot.  
  
Out of curiosity I grabbed the code from the web site (a 1.5Gb file) and
had a quick look. The bulk of the files are media, such as images,
movies, and 3D
[Maya](http://usa.autodesk.com/adsk/servlet/index?siteID=123112&id=7635018)
models. There\'s some nice stuff here. The actual tree itself is there
in [New Hampshire eXtended](http://www.phylosoft.org/forester/NHX.html)
format. Here it is displayed in TreeView X:  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_iyJqgNCMPmQWjDFlIz7EUmZTEYsk5ufFrgIlw6-10qzB_4RtagIjCsWkgIwMKYvGxV1h2Ro6Jwe28fmwGimHXSZd5p6LN_2mXBMBvjFRVskV_ItCNb3C32d4VxnDgV1BzeJV/s320/Untitled.png){#BLOGGER_PHOTO_ID_5298153393478847698
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 254px; height: 320px;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj_iyJqgNCMPmQWjDFlIz7EUmZTEYsk5ufFrgIlw6-10qzB_4RtagIjCsWkgIwMKYvGxV1h2Ro6Jwe28fmwGimHXSZd5p6LN_2mXBMBvjFRVskV_ItCNb3C32d4VxnDgV1BzeJV/s1600-h/Untitled.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
Here\'s the NHX tree itself.  
  

::: {style="font-family:Courier, fixed;font-size:10px"}
  
((((((((((((((((((((((((((((((Antelope:25.38857142856932
\[&&NHX:id=51129:tol=Y \], Sheep:25.38857142856932
\[&&NHX:id=51093:tol=Y \]):4.231428571428751 \[&&NHX:id=51154 \],
Cow:29.619999999998072 \[&&NHX:id=51150 \])Bovidae:33.26333333333336
\[&&NHX:id=50878:tol=Y \], Pig:62.883333333331485 \[&&NHX:id=51287:tol=Y
\]):0.978333333333334, Hippopotamus:63.86166666666491 \[&&NHX:id=30366
\]):2.445833333333335, Camel:66.30749999999811 \[&&NHX:id=30350:tol=Y
\])Artiodactyla:7.337500000000006 \[&&NHX:id=15976:tol=Y \],
Humpback_whale:73.64499999999816 \[&&NHX:id=16054 \]):9.663854166666676
\[&&NHX:id=15975 \], (((Horse:72.14374999999836 \[&&NHX:id=16255 \],
Rhino:72.14374999999836 \[&&NHX:id=16262
\])Perissodactyla:5.153125000000017 \[&&NHX:id=15980:tol=Y \],
Elephant:77.29687499999827 \[&&NHX:id=22667:tol=Y \]):4.294270833333347
\[&&NHX:id=15979 \], Aardvark:81.59114583333152 \[&&NHX:id=16881
\]):1.717708333333339):15.761701388888907 \[&&NHX:id=15974 \],
((((Brown_bear:40.2599999999984 \[&&NHX:id=123666:tol=Y \],
Polar_bear:40.2599999999984 \[&&NHX:id=123667:tol=Y
\])Ursidae:11.18333333333332 \[&&NHX:id=16015:tol=Y \],
Seal:51.443333333331715 \[&&NHX:id=16020 \]):4.473333333333327,
Dog:55.91666666666514 \[&&NHX:id=16013 \])Caniformia:11.18333333333332
\[&&NHX:id=16011 \], (Cat:40.259999999998215 \[&&NHX:id=123531:tol=Y \],
Lion:40.259999999998215 \[&&NHX:id=123566:tol=Y
\])Felidae:26.839999999999964 \[&&NHX:id=16006:tol=Y
\])Carnivora:31.9705555555556 \[&&NHX:id=15971:tol=Y
\]):0.15222222222222132, ((Mole:86.06453703703531 \[&&NHX:id=16213 \],
Shrew:86.06453703703531 \[&&NHX:id=16223 \]):3.759497354497354,
Hedgehog:89.82403439153265 \[&&NHX:id=16211
\])Insectivora:9.398743386243385 \[&&NHX:id=15968:tol=Y
\]):0.3805555555555533, (((Chimpanzee:9.143333333331611 \[&&NHX:id=26565
\], Human:9.143333333331611 \[&&NHX:id=16421:tol=Y \]):82.69666666666664
\[&&NHX:id=16412 \], Tree_shrew:91.83999999999833 \[&&NHX:id=50808
\]):4.1099999999999755 \[&&NHX:id=15962 \], Fruit_bat:95.94999999999834
\[&&NHX:id=16076 \]):3.6533333333333116 \[&&NHX:id=15961
\]):1.14166666666666, ((Hamster:56.967999999998256 \[&&NHX:id=16546 \],
Rat:56.96799999999821 \[&&NHX:id=50732 \])Eumuroida:33.211999999999804
\[&&NHX:id=16528 \], Rabbit:90.17999999999788 \[&&NHX:id=16227
\])Glires:10.565000000000104 \[&&NHX:id=15957 \]):16.484999999999623
\[&&NHX:id=15955 \], Kangaroo:117.22999999999797 \[&&NHX:id=16248
\]):31.38499999999999 \[&&NHX:id=15993 \], Platypus:148.61499999999816
\[&&NHX:id=16253:tol=Y \]):39.50999999999999 \[&&NHX:id=15990 \],
Megazostrodon:4.0625 \[&&NHX:id=15032:nsz=2:ncol=red:ext=Y
\])Cynodontia:32.5 \[&&NHX:id=15030 \], Dimetrodon:4.0625
\[&&NHX:id=14972:nsz=2:ncol=red:ext=Y \])Sphenacodontoidea:73.125
\[&&NHX:id=14971 \], (((((((((((((Flamingo:106.30859375000043
\[&&NHX:id=89474:tol=Y \], Toucan:106.3085937500002
\[&&NHX:id=93330:tol=Y \]):1.4296874999999905,
Penguin:107.73828125000037 \[&&NHX:id=57223:tol=Y
\])Neoaves:3.5742187499999765 \[&&NHX:id=26305:tol=Y \],
Duck:111.31250000000024 \[&&NHX:id=89298:tol=Y
\])Neognathae:4.289062499999972 \[&&NHX:id=26291 \],
Ostrich:115.60156250000016 \[&&NHX:id=26289:tol=Y
\])Neornithes:4.289062499999972 \[&&NHX:id=15834:tol=Y \],
Ichthyornis:4.386242378048764 \[&&NHX:id=15833:nsz=2:ncol=red:ext=Y
\])Euornithes_true_birds:12.867187499999915 \[&&NHX:id=15829 \],
Archaeopteryx:2.144531249999986 \[&&NHX:id=15824:nsz=2:ncol=red:ext=Y
\])Aves:12.867187499999915 \[&&NHX:id=15721:tol=Y \],
Tyrannosaurus_Rex:79.47061157226744
\[&&NHX:id=15889:nsz=2:ncol=red:ext=Y \]):74.99999999999773
\[&&NHX:id=15713 \], Diplodocus:157.62263488769486
\[&&NHX:id=15756:nsz=2:ncol=red:ext=Y \])Saurischia:9.374999999999716
\[&&NHX:id=15724 \], Iguanadon:165.44959259033112
\[&&NHX:id=15740:nsz=2:ncol=red:ext=Y \])Dinosauria:20.400000000000002
\[&&NHX:id=14883:tol=Y \], Crocodile:250.39999999999782 \[&&NHX:id=14868
\])Archosauria:22.950000000000003 \[&&NHX:id=14900:tol=Y \],
Snake:273.34999999999803 \[&&NHX:id=17563 \])Sauria:12.75
\[&&NHX:id=14913 \], Brouffia:1.275
\[&&NHX:id=14865:nsz=2:ncol=red:ext=Y \]):5.1 \[&&NHX:id=14864 \],
Tortoise:291.1999999999979 \[&&NHX:id=17631 \])Reptilia:2.55
\[&&NHX:id=14846 \])Amniota:56.25000000000091 \[&&NHX:id=14990:tol=Y \],
(Amphibians:317.3333333333312 \[&&NHX:id=14940 \],
Newt:317.3333333333311 \[&&NHX:id=82771
\])Living_amphibians:32.66666666666758 \[&&NHX:id=14997:tol=Y
\])Tetrapoda:9.00000000000009 \[&&NHX:id=14987 \],
Seymouriamorpha:14.610465116279109 \[&&NHX:id=17554:nsz=2:ncol=red:ext=Y
\]):40.87500000000041 \[&&NHX:id=14985 \],
(Acanthostega:1.8750000000000189
\[&&NHX:id=15016:tol=Y:nsz=2:ncol=red:ext=Y \],
Icthyostega:1.8750000000000189
\[&&NHX:id=15015:tol=Y:nsz=2:ncol=red:ext=Y
\]):0.7500000000000075):13.125000000000131 \[&&NHX:id=14976 \],
Panderichthys:2.2500000000000226 \[&&NHX:id=14951:nsz=2:ncol=red:ext=Y
\]):4.500000000000045 \[&&NHX:id=14950 \],
Eusthenopteron:2.2500000000000226 \[&&NHX:id=14949:nsz=2:ncol=red:ext=Y
\]):9.00000000000009 \[&&NHX:id=14948 \],
((Paddle_fish:363.6363636363626 \[&&NHX:id=68750 \],
Sturgeon:363.6363636363626 \[&&NHX:id=68749
\])Acipenseriformes:24.242424242424242 \[&&NHX:id=68726:tol=Y \],
Clown_fish:387.8787878787866 \[&&NHX:id=52149 \]):38.621212121213034
\[&&NHX:id=68709 \])Osteichthyes:9.00000000000009 \[&&NHX:id=14921 \],
Shark:435.5 \[&&NHX:id=14925 \])Node_1:13.944444444444489
\[&&NHX:id=14919 \], Cephalaspidida:19.261904761904795
\[&&NHX:id=16894:nsz=2:ncol=red:ext=Y \])Node_3:28.333333333333336
\[&&NHX:id=14840 \], Pteraspis:46.45061728395067
\[&&NHX:id=16929:nsz=2:ncol=red:ext=Y \])Node_1:9.444444444444445
\[&&NHX:id=14833 \], Lamprey:487.22222222222223 \[&&NHX:id=15919
\])Vertebrata:18.88888888888889 \[&&NHX:id=14829:tol=Y \],
Pikaia:506.1111111111113 \[&&NHX:id=14824 \]):158.00000000000003
\[&&NHX:id=14822 \], ((((((((Fruit_fly:339.4285714285717
\[&&NHX:id=10610 \], Peacock_butterfly:339.42857142857144
\[&&NHX:id=94054 \]):7.071428571428555 \[&&NHX:id=8224 \],
Wasp:346.5000000000002 \[&&NHX:id=11244 \]):28.28571428571422
\[&&NHX:id=8223 \], Cockroach:374.7857142857142 \[&&NHX:id=8544
\])Neoptera:7.071428571428555 \[&&NHX:id=8267:tol=Y \],
Giant_dragonfly:10.607142857142833 \[&&NHX:id=13265:nsz=2:ncol=red:ext=Y
\])Pterygota:98.80952380952378 \[&&NHX:id=8210:tol=Y \],
Brine_shrimp:480.6666666666665 \[&&NHX:id=6387 \]):43.81073446327684
\[&&NHX:id=2527 \], ((((Harevest_mite:496.40677966101725 \[&&NHX:id=2612
\], Spider:496.4067796610171 \[&&NHX:id=2788:tol=Y \]):8.864406779661008
\[&&NHX:id=2542 \], Harvestman:505.27118644067804 \[&&NHX:id=2556
\])Arachnida:8.864406779661008 \[&&NHX:id=2536:tol=Y \],
Sea_Scorpion:39.88983050847454 \[&&NHX:id=8174:nsz=2:ncol=red:ext=Y
\])Chelicerata:7.387005649717507 \[&&NHX:id=2535 \],
Millipede:521.5225988700563 \[&&NHX:id=52849
\]):2.954802259887003)Arthropoda:40.855932203389834
\[&&NHX:id=2469:tol=Y \], (Opabinia:555.9111111111108 \[&&NHX:id=20357
\], Velvet_worm:555.9111111111108 \[&&NHX:id=20356
\])Onychophora:9.422222222222217 \[&&NHX:id=2470:tol=Y
\]):70.55555555555556 \[&&NHX:id=2468 \], Acoel:635.8888888888889
\[&&NHX:id=20383 \]):28.222222222222225)Bilateria:85.88888888888889
\[&&NHX:id=2459:tol=Y \], Sponge:750.0 \[&&NHX:id=20438
\])Animals:2250.0 \[&&NHX:id=2374:tol=Y \], E.\_coli:3000.0
\[&&NHX:id=2306 \])Life_on_earth;
:::

  
  
It\'s great to see creative people tackling the challenge of displaying
the tree of life. I just not convinced that this is the best way to do
it.


Last night BBC One aired David Attenborough's Charles Darwin and the Tree of Life, which featured a lovely "fly through" the tree of life:In conjunction with the TV show, the Wellcome Trust has launched the Interactive Tree of Life, a Flash-based view of the tree of life. There's also a blog about the project. Here's a demo of the tree:The tree looks very nice, and a lot of work has gone into it, but I am somewhat underwhelmed.

Postagens de Rogue Scholar

OneZoom

Touching the tree of life

EOL Phylogenetic Tree Challenge

Tree of Life 0.1 - annotating the NCBI taxonomy

Thoughts on the Wellcome Interactive Tree of Life