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

# build a phylogenetic tree from nucleotide alignments

FastTree-2.1.9 -gtr -nt genes.fasta.aln > gene-tree.tre