sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

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

Author
A. Jesus Muñoz Pajares
Date of publication
2015-02-28 01:23:26
Maintainer
A.J. Muñoz-Pajares <ajesusmp@ugr.es>
License
GPL-2
Version
3.0.1

View on CRAN

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

Files in this package

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