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sidier (version 4.1.0)
Substitution and Indel Distances to Infer Evolutionary Relationships
Description
Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.
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4.1.0
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Install
install.packages('sidier')
Monthly Downloads
238
Version
4.1.0
License
GPL-2
Maintainer
AJ MuozPajares
Last Published
June 25th, 2021
Functions in sidier (4.1.0)
Search functions
Example_Spatial.plot_Alignment
example alignment #1 (fasta format)
NINA.thr
No Isolated Nodes Allowed network
FindHaplo
Find equal haplotypes
GetHaplo
Get sequences of unique haplotypes
MCIC
Modified Complex Indel Coding as distance matrix
SIC
Indel distances following the Simple Index Coding method
BARRIEL
Indel distances following Barriel method
FIFTH
Indel distances following the fifth state rationale
HapPerPop
Returns the number of haplotypes per population.
FilterHaplo
Filter haplotypes by occurrence
compare.dist
Threshold to discriminate species comparing intra- and interspecific distance distributions
inter.intra.plot
Histogram of the intra- and interspecific distances
get.majority.taxo
Get majority taxonomy for a sequence
ex_Coords
example coordinates
alignExample
example alignment #1 ('DNAbin' class)
assign.whole.taxo
Get taxonomy described in sequence names
ex_alignment1
example alignment #1
colour.scheme
internal function for node colour scheme
barcode.summary
Summary of the inter- and intraspecific distances
rule
Threshold to discriminate species.
pop.dist
Distances among populations
distance.comb
Distance matrices combination
barcode.gap
Barcode gap identification
mergeNodes
Merges nodes showing distance values equal to zero
mutation.network
Haplotype network depiction including mutations
genbank.sp.names
Species names from genbank accessions
barcode.quality
Estimates of barcode quality
filter.whole.taxo
Get consensus taxonomy
pie.network
Population network depiction including haplotype frequencies
perc.thr
Percolation threshold network
mutationSummary
Summary of observed mutations
double.plot
Haplotype and population networks including mutations and haplotype frequencies.
ex_BLAST
example BLAST output
nt.gap.comb
substitution and indel distance combinations
single.network.module
Get modules and network given a threshold
simuEvolution
Simulate sequences evolution
simplify.network
Network showing modules as nodes
sidier-package
SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
single.network
Plot a network given a threshold
spatial.plot
spatial plot of populations
zero.thr
Zero distance networks