sidier-package: SIDIER: Substitution and Indel Distances to Infer...
In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships
Description
Details
Author(s)
References
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. 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
sidier documentation built on June 25, 2021, 5:10 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Details Author(s) References
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. 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
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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