Nextflow Modules
Showing module(s) with keyword "gene evolution"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/hyphy/absrel | Process | positive selection branch-site selection gene evolution | aBSREL (adaptive Branch-Site Random Effects Likelihood) identifies instances where a proportion of sites along specific branches or lineages of a phylogeny have undergone positive selection. |
| nf-core/hyphy/busted | Process | positive selection gene-wide gene evolution | BUSTED (Branch-Site Unrestricted Statistical Test for Episodic Diversification) provides a gene-wide (not site-specific) test for positive selection by asking whether a gene has experienced positive selection at at least one site on at least one branch. |
| nf-core/hyphy/fel | Process | positive selection episodic selection gene evolution | The Fixed Effects Likelihood (FEL) method is used to identify individual codons that have been subject to pervasive diversifying or purifying selection. |
| nf-core/hyphy/fubar | Process | positive selection pervasive selection gene evolution pathogen evolution large datasets | FUBAR (Fast, Unconstrained Bayesian AppRoximation) uses a Bayesian approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. |
| nf-core/hyphy/gard | Process | recombination pre-processing selection inference gene evolution | GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence alignment for the presence of recombination and is extremely useful as a pre-processing step for selection inference. |
| nf-core/hyphy/meme | Process | positive selection episodic selection gene evolution | The Mixed Effects Model of Evolution (MEME) is used to identify individual codon sites subject to episodic or pervasive positive selection. |
| nf-core/hyphy/slac | Process | pervasive selection site selection gene evolution | The Single-Likelihood Ancestor Counting (SLAC) method is used to identify individual codon sites subject to pervasive diversifying or purifying selection. |