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
read more
http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html