Package: sidier 4.1.0

A.J. Muñoz-Pajares

sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework.

Authors:A. Jesus Muñoz Pajares

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sidier.pdf |sidier.html✨
sidier/json (API)
NEWS

# Install 'sidier' in R:
install.packages('sidier', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

35 exports 0.23 score 56 dependencies 1 mentions 36 scripts 219 downloads

Last updated 3 years agofrom:87831ca965. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-linuxNOTESep 01 2024

Exports:assign.whole.taxobarcode.gapbarcode.qualitybarcode.summaryBARRIELcolour.schemecompare.distdistance.combdouble.plotFIFTHfilter.whole.taxoFilterHaploFindHaplogenbank.sp.namesget.majority.taxoGetHaploHapPerPopinter.intra.plotMCICmergeNodesmutation.networkmutationSummaryNINA.thrnt.gap.combperc.thrpie.networkpop.distruleSICsimplify.networksimuEvolutionsingle.networksingle.network.modulespatial.plotzero.thr

Dependencies:apeaskpassbitopsclicodacolorspacecpp11curldigestdplyrfansifarvergenericsggmapggplot2gluegridBasegtablehttrigraphisobandjpegjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnetworknlmeopensslpillarpkgconfigplyrpngpurrrR6RColorBrewerRcpprlangscalesstatnet.commonstringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationshipssidier-package sidier
example alignment #1 ('DNAbin' class)alignExample
Get taxonomy described in sequence namesassign.whole.taxo
Barcode gap identificationbarcode.gap
Estimates of barcode qualitybarcode.quality
Summary of the inter- and intraspecific distancesbarcode.summary
Indel distances following Barriel methodBARRIEL
internal function for node colour schemecolour.scheme
Threshold to discriminate species comparing intra- and interspecific distance distributionscompare.dist
Distance matrices combinationdistance.comb
Haplotype and population networks including mutations and haplotype frequencies.double.plot
example alignment #1ex_alignment1
example BLAST outputex_BLAST
example coordinatesex_Coords
example alignment #1 (fasta format)Example_Spatial.plot_Alignment
Indel distances following the fifth state rationaleFIFTH
Get consensus taxonomyfilter.whole.taxo
Filter haplotypes by occurrenceFilterHaplo
Find equal haplotypesFindHaplo
Species names from genbank accessionsgenbank.sp.names
Get majority taxonomy for a sequenceget.majority.taxo
Get sequences of unique haplotypesGetHaplo
Returns the number of haplotypes per population.HapPerPop
Histogram of the intra- and interspecific distancesinter.intra.plot
Modified Complex Indel Coding as distance matrixMCIC
Merges nodes showing distance values equal to zeromergeNodes
Haplotype network depiction including mutationsmutation.network
Summary of observed mutationsmutationSummary
No Isolated Nodes Allowed networkNINA.thr
substitution and indel distance combinationsnt.gap.comb
Percolation threshold networkperc.thr
Population network depiction including haplotype frequenciespie.network
Distances among populationspop.dist
Threshold to discriminate species.rule
Indel distances following the Simple Index Coding methodSIC
Network showing modules as nodessimplify.network
Simulate sequences evolutionsimuEvolution
Plot a network given a thresholdsingle.network
Get modules and network given a thresholdsingle.network.module
spatial plot of populationsspatial.plot
Zero distance networkszero.thr