Man pages for sidier
Substitution and Indel Distances to Infer Evolutionary Relationships

alignExampleexample alignment #1 ('DNAbin' class)
barcode.gapBarcode gap identification
barcode.qualityEstimates of barcode quality
barcode.summarySummary of the inter- and intraspecific distances
BARRIELIndel distances following Barriel method
colour.schemeinternal function for node colour scheme
compare.distThreshold to discriminate species comparing intra- and...
distance.combDistance matrices combination
double.plotHaplotype and population networks including mutations and...
ex_alignment1example alignment #1
Example_Spatial.plot_Alignmentexample alignment #1 (fasta format)
ex_Coordsexample coordinates
FIFTHIndel distances following the fifth state rationale
FilterHaploFilter haplotypes by occurrence
FindHaploFind equal haplotypes
genbank.sp.namesSpecies names from genbank accessions
GetHaploGet sequences of unique haplotypes
HapPerPopReturns the number of haplotypes per population.
inter.intra.plotHistogram of the intra- and interspecific distances
MCICModified Complex Indel Coding as distance matrix
mergeNodesMerges nodes showing distance values equal to zero
mutation.networkHaplotype network depiction including mutations
mutationSummarySummary of observed mutations
NINA.thrNo Isolated Nodes Allowed network
nt.gap.combsubstitution and indel distance combinations
perc.thrPercolation threshold network
pie.networkPopulation network depiction including haplotype frequencies
pop.distDistances among populations
ruleThreshold to discriminate species.
SICIndel distances following the Simple Index Coding method
sidier-packageSIDIER: Substitution and Indel Distances to Infer...
simplify.networkNetwork showing modules as nodes
simuEvolutionSimulate sequences evolution
single.networkPlot a network given a threshold
single.network.moduleGet modules and network given a threshold
spatial.plotspatial plot of populations
zero.thrZero distance networks
sidier documentation built on July 10, 2018, 1:03 a.m.