Substitution and Indel Distances to Infer Evolutionary
Relationships
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Documentation for package ‘sidier’ version 4.1.0
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 |