Phylogenetic Clustering (Phyloclustering)
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Find the Best Solution of phyclust
Find the Consensus Sequence
Phyloclustering -- Phylogenetic Clustering
Boundary Methods for Population Proportions
Code Types of Dataset and Substitution Models
Colors for Identifying Clusters in Plots
Evolution Distance Model
EM Methods and Algorithms
EM Control
EM Control Generator
Identifiers for Evolution Models
Initialization Methods for EM Algorithms
Initialization Procedures for EM Algorithms
Label Method
Sequencing Error Model
Standard Codes and ids for Nucleotides, SNPs, Codon, Amino Acid and Ge...
Substitution Models for Mutation Processes
Coerce a Rooted Tree to a Star Tree in Class phylo
Bootstrap a seq.data from a Fitted Model.
Bootstrap Sequences from a Fitted Model and Star Tree.
Bootstrap a Star Tree from a Fitted Model.
Bootstrap Sequences from a Fitted Model.
Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)
Transfer Nucleotide Codes / nids and SNPs / sids
Great Pony 625 EIAV rev Dataset in the Fasta Format
Crohn's Disease SNP Dataset in the phylip Format
Great Pony 524 EIAV rev Dataset in the phylip Format
Read Data from Files by Formats and Return a seq.data Object
Write Data to Files by Formats
Generate Comprehensive Trees.
Generate Sequences Given a Rooted Tree.
Generate a Rooted Tree with a Star Shape
Generate Comprehensive Trees.
Get a Rooted Tree Height
Tzeng's Method: Finding the Best Number of Clusters
Tzeng's Method: Haplotype Grouping for SNP Sequences
Generating Samples under a Wright-Fisher Neutral Model of Genetic Vari...
Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, .....
Phylogenetic Analysis by Maximum Likelihood for Nucleotide Sequences
One E-Step of phyclust
Evolution Distance of Sequences
One EM-step of phyclust
Log-Likelihood of phyclust
One M-Step of phyclust
Transition Probabilities of phyclust Given Time
The Main Function of phyclust
The Main Function of phyclust for Sequencing Error Models
Update phyclust Results by the Sequencing Error Model
Update phyclust Results
Dots Plots of Sequences for Visual Comparisons
Gaps Plots of Sequences for Visual Comparisons
Plot Histogram to Compare Number of Mutations.
Plot an Unrooted Trees.
Struct Plots of Observations Based on Posterior Probabilities
Functions for Printing or Summarizing Objects According to Classes
Prune the Center Sequences Mu
Read seqgen's Results and Return a seq.data
Rescale a Rooted Tree's Height
Rand Index and Adjusted Rand Index
A Toy Dataset in Class seq.data
Seq-Gen
Transfer SNP codes (1, 2, -) and sids (0, 1, 2)
All Internal Functions of phyclust
All Internal Functions of Tzeng's Methods
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.