Phylotastic/Related Projects: Difference between revisions

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Here, we're cataloging and discussing how Phylotastic links to and builds upon other projects.

Some of those projects include:

Name What does it do? Strengths? Limitations? How does Phylotastic build upon, use or improve it?
Phylomatic Prunes megatrees into smaller trees, allows some file conversions Extremely easy to use add info here add info here
Tree of Life Web Uses a phylogenetic hierarchy to serves information on and illustrate all major groups of the tree of life High educational merit, substantial buy-in from taxonomic experts Phylogeny is static, infrequently updated and controlled by limited number of curators add info here
Treebase Add info here Add info here Add info here add info here
OpenTree Make a tree of everything, serve it up Add info here Add info here add info here
SADI (dead link?) strives towards high levels of interoperability of web services Add info here Add info here add info here
Galaxy probably the best example of a web-based biological analytical toolkit Widely used, well supported,good documentation Doesn't deal much with evolution or systematics add info here
iPlant Provides connected and collabroative environment for studying the organismal biology of plants: including modules for phenotype-genotype links, building big trees, linking trees to trait data, and visualizing phylogenies Add info here Add info here add info here
Encyclopedia of Life Provides an informational page for every one of the Earth's species High educational value, well-curated, good source of accurately identified images organized around the hierarchical ITIS taxonomy, but doesn't yet integrate phylogeny Probably the most obvious source for images or species-level data to map to tips of phylotasticized trees
Mesquite runs many types of analyses using phylogenies probably provides the most comprehensive and widely used tool for converting phylogenies among formats or linking character data to phylogenies Steep learning curve. Strongly encourages that the whole analysis pipeline reside in Mesquite. add info here
Phylogenetics Packages in R Provides a single framework that has many phylogenetic methods and visualizations Wide user community. Easily extensible. High barrier to entry and use. add info here
Timetree Add info here Add info here Add info here add info here
PHLAWD Add info here Add info here Add info here add info here
PHYUTILITY Add info here Add info here Add info here add info here
Tolkin Add info here Add info here Add info here add info here
Phylota Add info here Add info here Add info here add info here
CIPRES Add info here Add info here Add info here add info here
BioPortal Add info here Add info here Add info here add info here
www.phylogeny.fr Add info here Add info here Add info here add info here
Arbor develop user friendly portal for comparative methods Add info here Add info here add info here
Fossil Calibration Database NESCent Working Group Add info here Add info here Add info here add info here
Phenoscape Links lots of data from morphological phylogenetic studies to data from developmental biology and genetics Add info here Add info here add info here

Possible questions to address in the discussion section of the manuscript

We should be able to distill this table into text answering the following questions:

Which are the most important other projects to which Phylotastic links, connects or improves?

Another thing is that we will need to pick and choose wisely which software to make phylotastic interoperable with. Clearly we can't do everything; we need to pick stuff that compliments our own toolkit. -- Matt Pennell

How else have people tried (with or without success) to link phylogenies to other data or to make phylogenies more widely accessible?

Who else has created a component-based framework for the integration of biological data?

What other attempts have been made to develop automated tools to integrate phylogenetic knowledge?

How does the Phylotastic approach build upon, connect, or leverage these other initiatives?

The idea that there is a tree of life that users can slice and dice to their own needs. My sense is that there are either portals that allow people to do the slicing and dicing on their own trees (e.g. the computational portals) and ones that have an underlying notion of a tree of life without making it easily sliceable and diceable, but not both. Perhaps. -- Rutger

Its focus on modularity. It will have an overall architecture, but with discrete components that work well on their own (like TNRS). This is different from something like Mesquite, where if you want its stochastic character simulator you basically have to use the rest of Mesquite (in theory you could pull this module out, but it appears hard enough to have never been done in practice). -- Brian O'Meara

What does Phylotastic do that other projects don't?

What does Phylotastic need to do or achieve in order for it to be widely adopted?

One thing that will be key for the phylotastic manuscript is to make it stand out against this background of software packages. It might also be worth looking into some of the manuscripts and/or websites associated with various tools to try and figure out what is it about the software that makes them widely adopted (or perhaps more importantly, not). is it the presentation of the material, the ease of use, the journal in which the software was presented, how comprehensive the program is, the amount of effort geared towards building the community of users, etc, etc. seems more like marketing than science but I do think it is important if we want people to use our stuff. -- Matt Pennell

What will be the ultimate impact of Phylotastic?