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ropensci

treeio:Base Classes and Functions for Phylogenetic Tree Input and Output

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

Maintained by Guangchuang Yu. Last updated 5 months ago.

softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees

102 stars 12.46 score 1.3k scripts 122 dependents

snoweye

phyclust:Phylogenetic Clustering (Phyloclustering)

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

Maintained by Wei-Chen Chen. Last updated 2 years ago.

9 stars 8.45 score 126 scripts 8 dependents

helixcn

phylotools:Phylogenetic Tools for Eco-Phylogenetics

A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.

Maintained by Jinlong Zhang. Last updated 6 months ago.

11 stars 7.31 score 368 scripts

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