What is UniFrac distance?

What is UniFrac distance?

The unique fraction metric, or UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both.

What does unweighted UniFrac measure?

UniFrac is a distance metric used for comparing biological communities. Both weighted (quantitative) and unweighted (qualitative) variants of UniFrac are widely used in microbial ecology, where the former accounts for abundance of observed organisms, while the latter only considers their presence or absence.

What is UniFrac PCoA?

UniFrac is a β-diversity measure that uses phylogenetic information to compare environmental samples. UniFrac, coupled with standard multivariate statistical techniques including principal coordinates analysis (PCoA), identifies factors explaining differences among microbial communities.

Is Bray Curtis phylogenetic?

First, the Bray-Curtis dissimilarity creates a matrix in function of the how much the samples are different. Whereas the UniFrac measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment.

What is a distance tree?

Distance Methods. Tree is built using distances rather than original data. Only possible method if data were originally distances: { immunological cross-reactivity. { DNA annealing temperature.

What is Faith’s phylogenetic diversity?

The most widely used phylogenetic metric is Faith’s phylogenetic diversity (PD) (Faith 1992) which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species in the target assemblage. Like species richness, Faith’s PD does not consider species abundances.

What is principal coordinate analysis?

Principal Coordinate Analysis (often referred to as PCoA) is aimed at graphically representing a resemblance matrix between p elements (individuals, variables, objects, among others). The algorithm can be divided into three steps: Computation of a distance matrix for the p elements.

What does Bray Curtis measure?

Named after J. Roger Bray and John Thomas Curtis, the Bray-Curtis Dissimilarity is a way to measure the dissimilarity between two different sites. It’s often used in ecology and biology to quantify how different two sites are in terms of the species found in those sites.

How do you read a distance tree?

to get the distance between them, you simply sum up the length of the branches between them, i.e., you sum the horisontal branches leading from one of them to the root and then do the same for the other.

How do you calculate phylogenetic diversity?

Faith (1992) defined the phylogenetic diversity of a set of species as equal to the sum of the lengths of all those branches on the tree that span the members of the set. The branch lengths on the tree are informative because they count the relative number of new features arising along that part of the tree.

How to calculate weighted or unweighted UniFrac distance?

UniFrac-methods: Calculate weighted or unweighted (Fast) UniFrac distance for… This function calculates the (Fast) UniFrac distance for all sample-pairs in a phyloseq-class object. (Required). phyloseq-class, containing at minimum a phylogenetic tree ( phylo-class) and contingency table ( otu_table-class ).

How to calculate the UniFrac distance for phyloseq?

UniFrac: Calculate weighted or unweighted (Fast) UniFrac distance for all sample pairs. This function calculates the (Fast) UniFrac distance for all sample-pairs in a phyloseq-class object. ## S3 method for class ‘phyloseq’: UniFrac (physeq, weighted = FALSE, normalized = TRUE, parallel = FALSE, fast = TRUE)

How is a distance matrix created in UniFrac?

If there are several different samples, a distance matrix can be created by making a tree for each pair of samples and calculating their UniFrac measure. Subsequently, standard multivariate statistical methods such as data clustering and principal co-ordinates analysis can be used.

Is there a generalized version of the UniFrac?

In 2012, a generalized UniFrac version, which unifies the weighted and unweighted UniFrac distance in a single framework, was proposed. The weighted and unweighted UniFrac distance place too much weight on either abundant lineages or rare lineages.