Package for evolutionary reconstruction and bar code analyses based on substitutions and insertion-deletion (indels) in a distance-based framework.
The DESCRIPTION file: sidier sidier 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.
Mu<U+00F1>oz-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