sidier (version 2.2)

MCIC: Modified Complex Indel Coding as distance matrix

Description

This function computes an indel distance matrix following the rationale of the Modified Complex Indel Coding (Muller, 2006) to estimate transition matrices.

Usage

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

Arguments

inputFile

the name of the fasta file to be analysed.

align

the name of the alignment to be analysed. 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.

Details

It is recommended to estimate this distance matrix after removing repeated sequences from the alignment. Repeated sequences increase computation time but do not provide additional information (because they produce duplicated rows and columns in the final distance matrix).

References

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

Examples

cat(">Population1_sequence1",
"A-AGGGTC-CT---G",
">Population1_sequence2",
"TAA---TCGCT---G",
">Population1_sequence3",
"TAAGGGTCGCT---G",
">Population1_sequence4",
"TAA---TCGCT---G",
">Population2_sequence1",
"TTACGGTCG---TTG",
">Population2_sequence2",
"TAA---TCG---TTG",
">Population2_sequence3",
"TAA---TCGCTATTG",
">Population2_sequence4",
"TTACGGTCG---TTG",
">Population3_sequence1",
"TTA---TCG---TAG",
">Population3_sequence2",
"TTA---TCG---TAG",
">Population3_sequence3",
"TTA---TCG---TAG",
">Population3_sequence4",
"TTA---TCG---TAG",
     file = "ex3.fas", sep = "")

# Reading the alignment directly from file and saving no output file:
MCIC (input="ex3.fas", saveFile = FALSE)

# Analysing the same dataset, but using only unique sequences:
uni<-GetHaplo(inputFile="ex3.fas",saveFile=FALSE)
MCIC (align=uni, saveFile = FALSE)