sidier-package: SIDIER: Substitution and Indel Distances to Infer...
In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships
sidier-package 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:
This package was not yet installed at build time.
Index: This package was not yet installed at build time.
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.J. Muñoz-Pajares [cre, aut]
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.
sidier documentation built on June 8, 2025, 11:41 a.m.
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| sidier-package | 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:
This package was not yet installed at build time.
Index: This package was not yet installed at build time.
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.J. Muñoz-Pajares [cre, aut]
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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