sidier: Substitution and Indel Distances to Infer Evolutionary Relationships
Version 3.0.1

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.

AuthorA. Jesus Muñoz Pajares
Date of publication2015-02-28 01:23:26
MaintainerA.J. Muñoz-Pajares <ajesusmp@ugr.es>
LicenseGPL-2
Version3.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sidier")

Getting started

Package overview

Popular man pages

Example_Spatial.plot_Alignment: example alignment #1 (fasta format)
GetHaplo: Get sequences of unique haplotypes
HapPerPop: Returns the number of haplotypes per population.
perc.thr: Percolation threshold network
pie.network: Population network depiction including haplotype frequencies
pop.dist: Distances among populations
single.network: Plot a network given a threshold
See all...

All man pages Function index File listing

Man pages

alignExample: example alignment #1 ('DNAbin' class)
BARRIEL: Indel distances following Barriel method
colour.scheme: internal function for node colour scheme
distance.comb: Distance matrices combination
double.plot: Haplotype and population networks including mutations and...
ex_alignment1: example alignment #1
Example_Spatial.plot_Alignment: example alignment #1 (fasta format)
ex_Coords: example coordinates
FIFTH: Indel distances following the fifth state rationale
FindHaplo: Find equal haplotypes
GetHaplo: Get sequences of unique haplotypes
HapPerPop: Returns the number of haplotypes per population.
MCIC: Modified Complex Indel Coding as distance matrix
mergeNodes: Merges nodes showing distance values equal to zero
mutation.network: Haplotype network depiction including mutations
mutationSummary: Summary of observed mutations
NINA.thr: No Isolated Nodes Allowed network
nt.gap.comb: substitution and indel distance combinations
perc.thr: Percolation threshold network
pie.network: Population network depiction including haplotype frequencies
pop.dist: Distances among populations
SIC: Indel distances following the Simple Index Coding method
sidier-package: SIDIER: Substitution and Indel Distances to Infer...
simplify.network: Network showing modules as nodes
simuEvolution: Simulate sequences evolution
single.network: Plot a network given a threshold
spatial.plot: spatial plot of populations
zero.thr: Zero distance networks

Functions

BARRIEL Man page Source code
Example_Spatial.plot_Alignment Man page
FIFTH Man page Source code
FindHaplo Man page Source code
GetHaplo Man page Source code
HapPerPop Man page Source code
MCIC Man page Source code
NINA.thr Man page Source code
SIC Man page Source code
alignExample Man page
colour.scheme Man page Source code
distance.comb Man page Source code
double.plot Man page Source code
ex_Coords Man page
ex_alignment1 Man page
mergeNodes Man page Source code
mutation.network Man page Source code
mutationSummary Man page Source code
nt.gap.comb Man page Source code
perc.thr Man page Source code
pie.network Man page Source code
pop.dist Man page Source code
sidier Man page
sidier-package Man page
simplify.network Man page Source code
simuEvolution Man page Source code
single.network Man page Source code
spatial.plot Man page Source code
zero.thr Man page Source code

Files

inst
inst/CITATION
NAMESPACE
NEWS
data
data/Example_Spatial.plot_Alignment.txt.gz
data/ex_Coords.txt.gz
data/ex_alignment1.rda
R
R/pie.network.R
R/single.network.R
R/mergeNodes.R
R/BARRIEL.R
R/nt.gap.comb.R
R/MCIC.R
R/pop.dist.R
R/double.plot.R
R/simuEvolution.R
R/simplify.network.R
R/GetHaplo.R
R/SIC.R
R/distance.comb.R
R/perc.thr.R
R/mutationSummary.R
R/zero.thr.R
R/spatial.plot.R
R/FIFTH.R
R/HapPerPop.R
R/mutation.network.R
R/colour.scheme.R
R/NINA.thr.R
R/FindHaplo.R
MD5
DESCRIPTION
man
man/alignExample.Rd
man/pie.network.Rd
man/zero.thr.Rd
man/ex_alignment1.Rd
man/NINA.thr.Rd
man/single.network.Rd
man/colour.scheme.Rd
man/simuEvolution.Rd
man/BARRIEL.Rd
man/distance.comb.Rd
man/FIFTH.Rd
man/mergeNodes.Rd
man/pop.dist.Rd
man/Example_Spatial.plot_Alignment.Rd
man/sidier-package.Rd
man/mutation.network.Rd
man/HapPerPop.Rd
man/SIC.Rd
man/mutationSummary.Rd
man/FindHaplo.Rd
man/ex_Coords.Rd
man/perc.thr.Rd
man/GetHaplo.Rd
man/MCIC.Rd
man/double.plot.Rd
man/spatial.plot.Rd
man/nt.gap.comb.Rd
man/simplify.network.Rd
sidier documentation built on May 20, 2017, 12:47 a.m.

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