sidier (version 1.0)

MCIC: Modified Complex Indel Coding as distance matrix

Description

This function computes the insertion-deletion (indel) distance matrix following the rationale of the Modified Complex Indel Coding (Muller, 2006) to estimate transition matrices, as described in Munoz-Pajares.

Usage

MCIC(readfile = T, input = NA, align = NA, saveFile = T, outname = paste(input, "IndelDistanceMatrixMullerMod.txt"))

Arguments

readfile

a logical; if TRUE (default) input alignment is provided as a fasta format in a text file. If FALSE, the alignment is provided as an R object.

input

the name of the fasta file to be analysed.

align

the name of the alignment to be analysed (if "readfile" is set to FALSE,). See "read.dna" in ape package for details about reading alignments.

saveFile

a logical; if TRUE (default), function output is saved as a text file.

outname

if "SaveFile" is set to TRUE (default), contains the name of the output file.

Value

• A matrix containing the genetic distances estimated as indels pairwise differences.

References

Muller K. (2006). Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution, 38, 667-676.

Munoz-Pajares, AJ. SIDIER: Substitution and Indel Distances to Infer Evolutionary Relationships.

Examples

cat(">Population1_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence2",
"TTATAGCTGTCGGGCTA------GTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence3",
"GGGGAGCTGTCGGGCTAGTAGCTGTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population1_sequence4",
"TTATAGCTGTCGGGCTA------GTATCAGTCGTACGTAGTAGTCGTGTCGATCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population2_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population2_sequence2",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGA----------GTAGAGTATG",
">Population2_sequence3",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAAAAAA",
">Population2_sequence4",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATCAATATTATATCGGCGATGCGTAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence1",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence2",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence3",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
">Population3_sequence4",
"TTATAGCTGTCGGGCTAGTAGCTGTATCAGTC--------------------TCGATGGCGCGGCGCATC--------------------TAGCGCTAGCTGATGCTAGTAGCGTAGAGTATG",
     file = "ex2.fas", sep = "")

# Reading the alignment directly from file and saving no output file:
MCIC (input="ex2.fas", saveFile = FALSE)