Compiling FastTree
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.[1]
Installed Version♯
FastTree 2.1.8 is installed on Proteus. Use this modulefile:
fasttree/gcc/2.1.8
Compiling♯
See: http://www.microbesonline.org/fasttree/#Install -- there is also a pre-compiled executable available for download.
Rather than typing the one-liner, create a Makefile:
CC = gcc
CFLAGS = -O3 -march=corei7-avx -fopenmp -DOPENMP -finline-functions -funroll-loops -Wall
LIBS = -lm
FastTree: FastTree.c
$(CC) $(CFLAGS) -o $@ $^ $(LIBS)
Then, type "make" to build. The excutable is named "FastTree".
Running♯
Since FastTree can run multithreaded, be sure to specify the "shm"
parallel environment (PE). To use a specific number of threads, an
environment variable must be set; there is no command line option. E.g.
to run with 8 threads (on 8 cores):
#$ -pe shm 8
...
export OMP_NUM_THREADS=$NSLOTS