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miLineage
Provides knowledge towards understanding the roles of microbes in the underlying disease mechanism. miLineage develops a general framework to: (a) perform robust association tests for the microbial community that exhibits arbitrary inter-taxa dependencies; (b) localize lineages on the taxonomic tree that are associated with covariates (e.g. disease status); (c) assess the overall association of the whole microbial community with the covariates. Unlike existing methods for microbiome association analysis, this framework does not make any distributional assumptions on the microbiome data; it allows for the adjustment of confounding variables and accommodates excessive zero observations and it incorporates taxonomic information.
phyloGenerator
An easy way for ecologists to make realistic, tenable phylogenies. With phyloGenerator, you can download real DNA sequence data for your species of interest, and then generate a calibrated phylogeny using a defensible constraint tree. Your phylogeny may not be 'correct', but it will have branch lengths based on DNA data and its topology will be safe. It'll be a 'real' phylogeny, not a best-guess from taxonomy filled with polytomies. You don't need to have an advanced knowledge of phylogenetics to use phyloGenerator. Just download the program, follow the guide, and you can build a phylogeny in minutes.
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