R: Substitution and Indel Distances to Infer Evolutionary Relationships

# Substitution and Indel Distances to Infer Evolutionary Relationships

## Documentation for package ‘sidier’ version 4.1.1

- DESCRIPTION file

## Help Pages

sidier-package | SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
alignExample | example alignment #1 ('DNAbin' class)
assign.whole.taxo | Get taxonomy described in sequence names
barcode.gap | Barcode gap identification
barcode.quality | Estimates of barcode quality
barcode.summary | Summary of the inter- and intraspecific distances
BARRIEL | Indel distances following Barriel method
colour.scheme | internal function for node colour scheme
compare.dist | Threshold to discriminate species comparing intra- and interspecific distance distributions
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_BLAST | example BLAST output
ex_Coords | example coordinates
FIFTH | Indel distances following the fifth state rationale
filter.whole.taxo | Get consensus taxonomy
FilterHaplo | Filter haplotypes by occurrence
FindHaplo | Find equal haplotypes
genbank.sp.names | Species names from genbank accessions
get.majority.taxo | Get majority taxonomy for a sequence
GetHaplo | Get sequences of unique haplotypes
HapPerPop | Returns the number of haplotypes per population.
inter.intra.plot | Histogram of the intra- and interspecific distances
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
rule | Threshold to discriminate species.
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
single.network.module | Get modules and network given a threshold
spatial.plot | spatial plot of populations
zero.thr | Zero distance networks