TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

Tree-Puzzle Documentation
Tree-Puzzle website

Tree-Puzzle on Biowulf has been built with MPI for parallel runs. To submit a job on Biowulf, create a command file similar to the following:

-------------------Sample command file for Tree-Puzzle-----------------------
#!/bin/csh
#PBS -N Ppuzzle
#PBS -m be
#PBS -k oe

set path = (/usr/local/mpich/bin $path)

cd /data/username/tree/

mpirun -machinefile $PBS_NODEFILE -np $np /usr/local/bin/ppuzzle << EOF
primates.b
y
EOF

-----------------------------------------------------------------------------

Submit this job using the qsub command, e.g:

qsub -v np=4 -l nodes=2 command-file

Tree-Puzzle has many options. A summary is below:

GENERAL OPTIONS
 b                   Type of analysis?    Tree reconstruction
 k                Tree search procedure?  Quartet puzzling
 v       Approximate quartet likelihood?  No
 u             List unresolved quartets?  No
 n             Number of puzzling steps?  1000
 j             List puzzling step trees?  No
 o                  Display as outgroup?  Gibbon
 z     Compute clocklike branch lengths?  No
 e                  Parameter estimates?  Approximate (faster)
 x            Parameter estimation uses?  Neighbor-joining tree
SUBSTITUTION PROCESS
 d          Type of sequence input data?  Nucleotides
 m                Model of substitution?  HKY (Hasegawa et al. 1985)
 t    Transition/transversion parameter?  Estimate from data set
 f               Nucleotide frequencies?  Estimate from data set
RATE HETEROGENEITY
 w          Model of rate heterogeneity?  Uniform rate

--------------------------------------------------------
#!/bin/csh
#PBS -N Ppuzzle
#PBS -m be
#PBS -k oe

set path = (/usr/local/mpich/bin $path)

cd /data/username/tree/

mpirun -machinefile $PBS_NODEFILE -np $np /usr/local/bin/ppuzzle << EOF
primates.b
n
8000
y
EOF
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