如何计算序列间的种内和种间遗传距离 How to Calcula

step 1. Prepare the distance matrix.

Tool： DistanceMatrix In DECIPHER(R package)

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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")

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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;

 

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

Tools: Excel, SpeciesIdentify in TaxonDNA

使用数组公式 使用excel数组公式

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-coordinateMin-inter distance.

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