Definitions - zwickl/terraphy GitHub Wiki
Terms used in terrace theory and the Terraphy software
A subset of columns of an alignment. May or may not correspond to an actual gene. Equivalent to what is commonly termed a "partition" in multilocus phylogenetic analyses.
A presence/absence summary of which loci are sampled for each taxon. The coverage pattern of a dataset determines its terraces properties.
The "focal" tree of a terrace analysis. Provided to Terraphy by the user. All functions pertain to the terrace on which this parent tree lies. Any parent tree from a given terrace will give identical results.
A single taxon that has been sampled for every locus. Such a taxon should be used to outgroup root the user-provided parent tree. Rooting with any reference (fully sampled) taxon will give equivalent results in Terraphy.
Model-based partitioned phylogenetic analyses must make an assumption about how the edge lengths estimated for each edge for each locus relate to one another. Any inference software may implement one or more of these:
A single set of edge lengths is shared by all loci. This model DOES NOT generate terraces and estimates the fewest number of parameters, but cannot accommodate among-locus rate variation.
Each edge has its own independent edge length estimated for each locus. Use of this model is REQUIRED for terraces to exist. Estimates a very large number of parameters.
A single set of mean edge lengths is estimated, and each locus has an estimated multiplier parameter that allows it to evolve more slowly or more quickly than the mean rate. this model DOES NOT generate terraces, and estimates a modest number of parameters, while still accommodating among-locus rate variation.