Initial commit. This version can use 1,500 taxa and unlimited checkpoint

cycles.
dosreislab · Aug 4, 2024 · f4d8ca1 · f4d8ca1
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diff --git a/README.md b/README.md
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+MCMCtree is a Bayesian MCMC program for estimation of species divergence times using molecular and trait data. MCMCtree was written by Ziheng Yang from University College London. This is a fork of MCMCtree version 4.9j with small modifications suitable for large-scale analyses. The latest version can be found in [PAML's repository](https://github.com/abacus-gene/paml).
diff --git a/src/Makefile b/src/Makefile
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+PRGS =  mcmctree 
+CC = cc # cc, gcc, cl # if running on an intel cluster, check if you can compile with the intel compiler, icc
+
+CFLAGS = -O3
+#CFLAGS = -fast # this flag is for the intel compiler
+
+LIBS = -lm # -lM
+
+all : $(PRGS)
+
+mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
+	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
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		MCMCtree is a Bayesian MCMC program for estimation of species divergence times using molecular and trait data. MCMCtree was written by Ziheng Yang from University College London. This is a fork of MCMCtree version 4.9j with small modifications suitable for large-scale analyses. The latest version can be found in [PAML's repository](https://github.com/abacus-gene/paml).