DiceDist
Filed in: C++
This program calculates Dice's
distance measure among all pairs of individuals from a population,
and outputs a triangle distance matrix suitable for use in Neighbor
or other phylogeny programs.
Requires the libsequence C++ library.
Version 1: Assumes dominant markers and requires SimDataDip for use on dominant markers.
Reads ms-formatted coalescent simulations from stdout. Requires specification of the number of populations, e.g.:
ms 20 1 -t 5 | dice -I 1 10
runs DiceDist on a single ms coalescent simulation of 20 alleles combined to form 10 dominant haplotypes.
Compiles with:
g++ -I. -I.. -I/usr/local/include -Wall -W -ansi -pedantic -DNDEBUG -O2 -c dist.cc SimDataDIP.cc
g++ -DNDEBUG -O2 -o dice dist.o SimDataDIP.o -lsequence
Download:
dist.cc
Version 2:
Same format, but assumes codominant markers.
Compiles with:
g++ -I. -I.. -I/usr/local/include -Wall -W -ansi -pedantic -DNDEBUG -O2 -c dist_cod.cc
g++ -DNDEBUG -O2 -o diceCod dist_cod.o -lsequence
Download
dist_cod.cc