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sidier (version 4.1.1)

Substitution and Indel Distances to Infer Evolutionary Relationships

Description

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework as described in Muñoz-Pajares (2013) .

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Version

Install

install.packages('sidier')

Monthly Downloads

133

Version

4.1.1

License

GPL-2

Maintainer

AJ MuozPajares

Last Published

June 6th, 2025

Functions in sidier (4.1.1)

distance.comb

Distance matrices combination
barcode.quality

Estimates of barcode quality
ex_BLAST

example BLAST output
compare.dist

Threshold to discriminate species comparing intra- and interspecific distance distributions
assign.whole.taxo

Get taxonomy described in sequence names
barcode.gap

Barcode gap identification
colour.scheme

internal function for node colour scheme
barcode.summary

Summary of the inter- and intraspecific distances
alignExample

example alignment #1 ('DNAbin' class)
double.plot

Haplotype and population networks including mutations and haplotype frequencies.
mutationSummary

Summary of observed mutations
nt.gap.comb

substitution and indel distance combinations
inter.intra.plot

Histogram of the intra- and interspecific distances
filter.whole.taxo

Get consensus taxonomy
mergeNodes

Merges nodes showing distance values equal to zero
genbank.sp.names

Species names from genbank accessions
get.majority.taxo

Get majority taxonomy for a sequence
ex_alignment1

example alignment #1
ex_Coords

example coordinates
mutation.network

Haplotype network depiction including mutations
pop.dist

Distances among populations
rule

Threshold to discriminate species.
simuEvolution

Simulate sequences evolution
single.network

Plot a network given a threshold
zero.thr

Zero distance networks
perc.thr

Percolation threshold network
pie.network

Population network depiction including haplotype frequencies
single.network.module

Get modules and network given a threshold
spatial.plot

spatial plot of populations
simplify.network

Network showing modules as nodes
sidier-package

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
FilterHaplo

Filter haplotypes by occurrence
Example_Spatial.plot_Alignment

example alignment #1 (fasta format)
FIFTH

Indel distances following the fifth state rationale
BARRIEL

Indel distances following Barriel method
HapPerPop

Returns the number of haplotypes per population.
GetHaplo

Get sequences of unique haplotypes
SIC

Indel distances following the Simple Index Coding method
FindHaplo

Find equal haplotypes
MCIC

Modified Complex Indel Coding as distance matrix
NINA.thr

No Isolated Nodes Allowed network