phangorn - Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
Last updated 1 days ago
softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
16.68 score 206 stars 135 dependents 2.5k scripts 21k downloadskknn - Weighted k-Nearest Neighbors
Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
Last updated 1 days ago
nearest-neighbor
11.66 score 23 stars 41 dependents 4.6k scripts 35k downloadsapex - Phylogenetic Methods for Multiple Gene Data
Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
Last updated 1 years ago
6.40 score 5 stars 54 scripts 1.2k downloadstanggle - Visualization of Phylogenetic Networks
Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <doi:10.1093/bioinformatics/btq706>.
Last updated 5 months ago
softwarevisualizationphylogeneticsalignmentclusteringmultiplesequencealignmentdataimport
6.40 score 11 stars 38 scripts 191 downloads