BARRIEL                 Indel distances following Barriel method
Example_Spatial.plot_Alignment
                        example alignment #1 (fasta format)
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
NINA.thr                No Isolated Nodes Allowed network
SIC                     Indel distances following the Simple Index
                        Coding method
alignExample            example alignment #1 ('DNAbin' class)
colour.scheme           internal function for node colour scheme
distance.comb           Distance matrices combination
double.plot             Haplotype and population networks including
                        mutations and haplotype frequencies.
ex_Coords               example coordinates
ex_alignment1           example alignment #1
mergeNodes              Merges nodes showing distance values equal to
                        zero
mutation.network        Haplotype network depiction including mutations
mutationSummary         Summary of observed mutations
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
sidier-package          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
