| sidier-package {sidier} | R Documentation |
SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships
Description
Package for evolutionary reconstruction and bar code analyses based on substitutions and insertion-deletion (indels) in a distance-based framework.
Details
The DESCRIPTION file:
| Package: | sidier |
| Type: | Package |
| Title: | Substitution and Indel Distances to Infer Evolutionary Relationships |
| Version: | 4.1.0 |
| Date: | 2021-06-25 |
| Author: | A. Jesus Muñoz Pajares |
| Maintainer: | A.J. Muñoz-Pajares <ajesusmp@ugr.es> |
| Depends: | R (>= 3.5.0) |
| Imports: | ape, network, igraph, gridBase, grid, ggmap, ggplot2 |
| Encoding: | UTF-8 |
| Description: | Evolutionary reconstruction based on substitutions and insertion-deletion (indels) analyses in a distance-based framework. |
| License: | GPL-2 |
Index of help topics:
BARRIEL Indel distances following Barriel method
Example_Spatial.plot_Alignment
example alignment #1 (fasta format)
FIFTH Indel distances following the fifth state
rationale
FilterHaplo Filter haplotypes by occurrence
FindHaplo Find equal haplotypes
GetHaplo Get sequences of unique haplotypes
HapPerPop Returns the number of haplotypes per
population.
MCIC Modified Complex Indel Coding as distance
matrix
NINA.thr No Isolated Nodes Allowed network
SIC Indel distances following the Simple Index
Coding method
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
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.
ex_BLAST example BLAST output
ex_Coords example coordinates
ex_alignment1 example alignment #1
filter.whole.taxo Get consensus taxonomy
genbank.sp.names Species names from genbank accessions
get.majority.taxo Get majority taxonomy for a sequence
inter.intra.plot Histogram of the intra- and interspecific
distances
mergeNodes Merges nodes showing distance values equal to
zero
mutation.network Haplotype network depiction including mutations
mutationSummary Summary of observed mutations
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.
sidier-package 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
Functions can be classified according to the following groups:
- Barcode analysis:
barcode.gap;
barcode.quality;
barcode.summary;
compare.dist;
genbank.sp.names;
inter.intra.plot;
rule.
- Example files:
alignExample;
Example_Spatial.plot_Alignment;
ex_alignment1;
ex_Coords.
- Indel coding methods:
BARRIEL;
FIFTH;
MCIC;
SIC.
- Matrix/network manipulation:
distance.comb;
mergeNodes;
nt.gap.comb;
simplify.network.
- Network-from-distance methods:
NINA.thr;
perc.thr;
zero.thr;
single.network;
single.network.module.
- Network visualization:
mutation.network;
pie.network;
double.plot;
colour.scheme;
spatial.plot.
- Sequence/haplotype analysis:
FilterHaplo;
FindHaplo;
GetHaplo;
HapPerPop;
mutationSummary;
pop.dist;
simuEvolution.
Author(s)
A. Jesus Muñoz Pajares
Maintainer: A.J. Muñoz-Pajares <ajesusmp@ugr.es>
References
Muñoz-Pajares, A. J. (2013). SIDIER: substitution and indel distances to infer evolutionary relationships. Methods in Ecology and Evolution 4, 1195-1200. doi: 10.1111/2041-210X.12118