Phylotastic/Related Projects

About this Page

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 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 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