treespace is an R package for the comparison of phylogenetic trees. This web interface provides easy access to the resources implemented in the package.
The Help tab explains everything in more detail. Briefly:
Get started with the Tree landscape explorer tab. Here you can use the example datasets of Dengue fever trees or woodmice trees, or upload your own trees. You can visualise the relative distances between trees in 2D or 3D according to various metrics, and colour them by type (e.g. coloured by gene) or by statistical clustering methods.
View individual trees in the Tree viewer tab, including the overall median tree according to the Kendall Colijn metric, and a median tree per cluster if statistical clusters have been identified.
View collections of trees superimposed on each other in the densiTree viewer tab. This can give an idea of how similar or otherwise the trees are.
[statistical exploration of landscapes of phylogenetic trees]
treespace implements statistical tools for the exploration of sets of phylogenetic trees describing the evolutionary relationships between the same taxa. This web interface provides an easy access to the resources implemented in the package. Each tab is made of two panels: a sidebar used to choose inputs, analysis tools and aesthetics, and a main panel displaying results.
Tree landscape explorer
The Tree landscape explorer tab is where the whole tree space can be explored. Choose between a two- or three-dimensional plot to visualise the trees using Metric Multidimensional Scaling (MDS, a.k.a. Principal Coordinates Analysis, PCoA), which calculates the best reduced-spaced visualisation of the distances between trees. The sidebar contains the following sections:
treespace takes a list of phylogenetic trees as input. The user can choose between data distributed with the package, or provide input files. Two types of input files can be used:
R objects saved using the function save(x, file="x.RData") where 'x' is a list of trees of the class multiphylo (from the ape package. Accepted extensions are ".RData" and ".rda".
list of trees saved in a nexus file, e.g. using ape's function write.nexus(x, file="x.nex") in R.
Tree summary / metric: the method to be used to measure distances between tips of the trees. Choose from:
Kendall Colijn: the tree metric developed by Kendall & Colijn; used by default
Billera, Holmes, Vogtmann: the Billera, Holmes & Vogtmann tree metric (also known as the 'geodesic distance')
Robinson Foulds (unrooted): the Robinson Foulds tree metric. Note that this implementation of the metric (from the package phangorn) treats the trees as unrooted and uses the unweighted edge-count distance (Robinson Foulds 1981).
Tip-tip path distance (unrooted): metric by Steel and Penny which counts the number of internal nodes on the shortest path between each pair of tips. Along with its weighted version (below), this is also known as the tip distance, nodal distance, patristic distance and dissimilarity measure. Trees are treated as unrooted. (see ?nNodes in the package adephylo)
Tip-tip branch-length distance (unrooted): similar to the tip-tip path distance, but using the branch lengths instead of counting the edges. (see ?distTips in the package adephylo)
Abouheif test: the Abouheif test as presented in Pavoine et al. (2008) (see ?distTips in the package adephylo)
Sum of direct descendents: another test related to the Abouheif test (see ?distTips in the package adephylo)
Lambda: The value of lambda used in Kendall & Colijn's metric. Numbe