Table of Contents
What is a weighted UniFrac?
The weighted unifrac algorithm is implemented within mothur as the unifrac. weighted command. The algorithm represents an attempt to make a quantitative beta diversity measurement that can be seen as an extension of unweighted UniFrac . Lozupone et al.
What does unweighted UniFrac mean?
There are two versions of UniFrac distances: an unweighted UniFrac distance that considers only species presence and absence information and counts the fraction of branch length unique to either community, and a weighted UniFrac distance that uses species abundance information and weights the branch length with …
What is the difference between weighted and unweighted UniFrac?
Weighted-UniFrac takes into account the relative abundance of species/taxa shared between samples, whereas unweighted-UniFrac only considers presence/absence. Default is FALSE , meaning the unweighted-UniFrac distance is calculated for all pairs of samples.
What is UniFrac analysis?
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.
What does UniFrac distance measure?
UniFrac metric. 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 (Fig. 1).
What does UniFrac distance mean?
UniFrac is a distance metric used for comparing biological communities. It differs from dissimilarity measures such as Bray-Curtis dissimilarity in that it incorporates information on the relative relatedness of community members by incorporating phylogenetic distances between observed organisms in the computation.
Is Bray Curtis weighted?
The key difference between Bray Curtis and weighted UniFrac distance is that UniFrac is phylogenetically aware. This means it treats closely related organisms as more similar, while Bray-Curtis doesn’t weight them in the same way.
What is beta diversity microbiome?
While alpha diversity is a measure of microbiome diversity applicable to a single sample, beta diversity is a measure of similarity or dissimilarity of two communities. As for alpha diversity, many indices exist, each reflecting different aspects of community heterogeneity.
What is Shannon index microbiome?
In our study, microbiota diversity was quantified using Shannon index. This diversity index is a quantitative indicator of the number of different bacteria that are present in a stool sample, taking into account the uniformity in the distribution of these bacteria in these species [22].
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 (Fig. 1).
What does high Shannon index mean?
How to interpret the Shannon diversity index? The higher the index, the more diverse the species are in the habitat. If the index equals 0, only one species is present in the community. It may be easier to interpret the result if you calculate the evenness: E = H / ln(k) , where k is the number of species.
What is Shannon H?
Use the Shannon diversity index formula: H = -∑[(pi) × ln(pi)] Calculate the proportion (pi) of each species – divide the number of individuals in a species by the total number of individuals in the community. For each species, multiply the proportion by the logarithm of the proportion.
Is there a weighted version of UniFrac?
Additionally, there is a weighted version of the UniFrac metric which accounts for the relative abundance of each of the taxa within the communities. This is commonly used in metagenomic studies, where the number of metagenomic reads can be in the tens of thousands, and it is appropriate to ‘bin’ these reads into operational…
How do you find the distribution of UniFrac values?
By randomizing the sample classification of each taxon on the tree (leaving the branch structure unchanged) and creating a distribution of UniFrac distance values, one can obtain a distribution of UniFrac values. From this, a p-value can be given to the actual distance between the samples.
What is the difference between unweighted-UniFrac and weighted-UniFrac?
Weighted-UniFrac takes into account the relative abundance of species/taxa shared between samples, whereas unweighted-UniFrac only considers presence/absence. Default is FALSE, meaning the unweighted-UniFrac distance is calculated for all pairs of samples. (Optional). Logical.
What is fast Uni FRAC?
“Fast Uni Frac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and Phylo Chip data”. The ISME Journal. 4 (1): 17–27. doi: 10.1038/ismej.2009.97.