如何计算序列间的种内和种间遗传距离

How to Calculate the Max-intra and Min-inter Distance distribution?

 

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DECIPHER")

For older versions of R, please refer to the appropriate Bioconductor release.

step 1.     Prepare the distance matrix.

Tool： DistanceMatrix In DECIPHER (R package)

• library(DECIPHER)
• DNAStringSet=readDNAStringSet("S:/xxx.txt")
• a= DistanceMatrix(DNAStringSet,
•               type = "matrix",
•               includeTerminalGaps = FALSE,
•               penalizeGapLetterMatches = FALSE,
•               penalizeGapGapMatches = FALSE,
•               correction = "none",
•               processors = NULL,
•               verbose = TRUE)
• write.csv(a, file = "S:/xxxxxxx.csv")

 

step 2.     Search the intra- and inter Distances of all sequences

Tool: Excel

 

•   Use MAXIF and MINIF formula to get intra- and inter Distances for each sequence，公式请使用数组公式;

 

 

step 3.     Search Max-intra and Min-inter Distances for every species

Tools: Excel, SpeciesIdentify in TaxonDNA

 

•  Use Species Summary Function to get species name list;
• Use VLOOKUP formula to search Max-intra and Min-inter distance for every species (Notice that use Species name list as Lookup_value，and sort the previous intra- and inter Distances results by descending and scending to get the final maximum and minimum results;

 

 

step 4.     Draw scatter diagram.

The x-coordinate is Max-intra distane, The y-coordinate Min-inter distance.