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FastTree

Download and Install


# download C code
wget http://meta.microbesonline.org/fasttree/FastTree.c
 
# compile with double precision
gcc -DUSE_DOUBLE -O3 -finline-functions -funroll-loops -Wall -o FastTree-2.1.9 FastTree.c -lm

# compile parallel version
gcc -DOPENMP -DUSE_DOUBLE -fopenmp -O3 -finline-functions -funroll-loops -Wall -o FastTreePar-2.1.9 FastTree.c -lm

# set the maximum number of parallel threads to 4 (add to your .bashrc file)
export OMP_NUM_THREADS=4

# add path to your .bashrc file
export PATH=$HOME/tools/FastTree:$PATH

http://meta.microbesonline.org/fasttree/#Install

Run FastTree

# build a phylogenetic tree from nucleotide alignments
FastTree-2.1.9 -gtr -nt genes.fasta.aln > gene-tree.tre

http://meta.microbesonline.org/fasttree/#Usage
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