sidier (version 4.1.0)

Substitution and Indel Distances to Infer Evolutionary Relationships

Description

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

Copy Link

Version

Install

install.packages('sidier')

Monthly Downloads

154

Version

4.1.0

License

GPL-2

Maintainer

AJ MuozPajares

Last Published

June 25th, 2021

Functions in sidier (4.1.0)

Example_Spatial.plot_Alignment

example alignment #1 (fasta format)

NINA.thr

No Isolated Nodes Allowed network

FindHaplo

Find equal haplotypes

GetHaplo

Get sequences of unique haplotypes

MCIC

Modified Complex Indel Coding as distance matrix

SIC

Indel distances following the Simple Index Coding method

BARRIEL

Indel distances following Barriel method

FIFTH

Indel distances following the fifth state rationale

HapPerPop

Returns the number of haplotypes per population.

FilterHaplo

Filter haplotypes by occurrence

compare.dist

Threshold to discriminate species comparing intra- and interspecific distance distributions

inter.intra.plot

Histogram of the intra- and interspecific distances

get.majority.taxo

Get majority taxonomy for a sequence

ex_Coords

example coordinates

alignExample

example alignment #1 ('DNAbin' class)

assign.whole.taxo

Get taxonomy described in sequence names

ex_alignment1

example alignment #1

colour.scheme

internal function for node colour scheme

barcode.summary

Summary of the inter- and intraspecific distances

rule

Threshold to discriminate species.

pop.dist

Distances among populations

distance.comb

Distance matrices combination

barcode.gap

Barcode gap identification

mergeNodes

Merges nodes showing distance values equal to zero

mutation.network

Haplotype network depiction including mutations

genbank.sp.names

Species names from genbank accessions

barcode.quality

Estimates of barcode quality

filter.whole.taxo

Get consensus taxonomy

pie.network

Population network depiction including haplotype frequencies

perc.thr

Percolation threshold network

mutationSummary

Summary of observed mutations

double.plot

Haplotype and population networks including mutations and haplotype frequencies.

ex_BLAST

example BLAST output

nt.gap.comb

substitution and indel distance combinations

single.network.module

Get modules and network given a threshold

simuEvolution

Simulate sequences evolution

simplify.network

Network showing modules as nodes

sidier-package

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships

single.network

Plot a network given a threshold

spatial.plot

spatial plot of populations

zero.thr

Zero distance networks