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;
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-coordinateMin-inter distance.
