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sidier (version 2.0)

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.

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Version

Install

install.packages('sidier')

Monthly Downloads

166

Version

2.0

License

GPL (>= 2)

Maintainer

AJ MuozPajares

Last Published

March 30th, 2013

Functions in sidier (2.0)

nt.gap.comb

substitution and indel distance combinations

pop.dist

Distances among populations

sidier-package

SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships

MCIC

Modified Complex Indel Coding as distance matrix

single.network

Plot a network given a threshold

GetHaplo

Get sequences of unique haplotypes

perc.thr

Percolation threshold network

HapPerPop

Returns the number of haplotypes per population.

FindHaplo

Find equal haplotypes