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).
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softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
17.08 score 216 stars 133 dependents 4.4k scripts 27k downloadskknn - Weighted k-Nearest Neighbors
Weighted k-Nearest Neighbors for Classification, Regression and Clustering.
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nearest-neighbor
11.45 score 24 stars 26 dependents 5.1k scripts 15k downloads
tanggle - 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>.
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softwarevisualizationphylogeneticsalignmentclusteringmultiplesequencealignmentdataimportphylogenetic-networks
7.46 score 12 stars 69 scriptsapex - 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.
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7.03 score 5 stars 66 scripts 4.3k downloads