Substitution and Indel Distances to Infer Evolutionary Relationships

Documentation for package ‘sidier’ version 3.0.1

sidier-package	SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
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 haplotype frequencies.
Example_Spatial.plot_Alignment	example alignment #1 (fasta format)
ex_alignment1	example alignment #1
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	SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
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