⚠️There's a newer version (4.1.1) of this package.Take me there.

sidier (version 2.2)

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

SIDIER provides functions for reading and writing fasta sequences, finding unique haplotypes, estimating genetic distances based on gap positions and lengths, combining distance matrices and estimating and plotting percolation networks.

Copy Link

Version

Install

install.packages('sidier')

Monthly Downloads

166

Version

2.2

License

GPL (>= 2)

Maintainer

AJ MuozPajares

Last Published

July 1st, 2013

Functions in sidier (2.2)

mutationSummary

Summary of observed mutations

simuEvolution

Simulate sequences evolution

nt.gap.comb

substitution and indel distance combinations

distance.comb

Distance matrices combiantion

FindHaplo

Find equal haplotypes

HapPerPop

Returns the number of haplotypes per population.

BARRIEL

Indel distances following Barriel method

FIFTH

Indel distances following the fifth state rationale

single.network

Plot a network given a threshold

sidier-package

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships

SIC

Indel distances following the Simple Index Coding method

perc.thr

Percolation threshold network

GetHaplo

Get sequences of unique haplotypes

pop.dist

Distances among populations

MCIC

Modified Complex Indel Coding as distance matrix