Citation¶
distree is archived on Zenodo. Cite the release you used:
Ruiz-Rodriguez P, Coscolla M. distree: distance matrices from a phylogeny. PathoGenOmics Lab. doi:10.5281/zenodo.16811766
The repository carries a CITATION.cff,
so GitHub's "Cite this repository" button and most reference managers will
produce the entry for you.
Please record the version (distree --version) and the mode you used. A
patristic matrix, a topological one and a variance-covariance matrix are three
different objects, and "distances from the tree" does not say which.
Authors¶
Paula Ruiz-Rodriguez and Mireia Coscolla, I²SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain.
Background¶
The quantities distree computes are standard, and the terms are worth pinning down.
Patristic distance is the sum of branch lengths along the path between two tips. The name is Farris's.
Farris JS. A Method for Computing Wagner Trees. Systematic Zoology. 1970;19(1):83-92.
The variance-covariance matrix that --lmm writes is the covariance
structure implied by Brownian-motion trait evolution on a tree, which is what
makes it the C of a phylogenetic generalised least squares fit.
Felsenstein J. Phylogenies and the Comparative Method. The American Naturalist. 1985;125(1):1-15.
Grafen A. The phylogenetic regression. Philosophical Transactions of the Royal Society B. 1989;326(1233):119-157.
Midpoint rooting places the root at the middle of the longest tip-to-tip path.
Farris JS. Estimating Phylogenetic Trees from Distance Matrices. The American Naturalist. 1972;106(951):645-668.
Binary lifting is the technique behind the O(log n) ancestor queries. The
sparse-table formulation of the least-common-ancestor problem goes back to:
Bender MA, Farach-Colton M. The LCA Problem Revisited. LATIN 2000, Lecture Notes in Computer Science 1776, pp. 88-94.
Formats and downstream tools¶
The --lower output is PHYLIP's lower-triangular distance format:
Felsenstein J. PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics. 1989;5:164-166.