"PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data." (doc/pamlDOC.pdf)


"'Fitmodel' estimates the parameters of various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck (2004).  These models are especially useful as they accommodate site-specific switches between selection regimes without a priori knowledge of the positions in the tree where changes of selection regimes occurred.

The program will ask for two input files: a tree file and a sequence file.  The tree should be unrooted and in NEWICK format.  The sequences should be in PHYLIP interleaved or sequential format.  If you are planning to use codon-based models, the sequence length should be a multiple of 3.  The program provides four types of codon models: M1, M2, M2a, and M3 (see PAML manual).  Moreover, M2, M2a and M3 can be combined with 'switching' models (option 'M').  Two switching models are implemented: S1 and S2.  S1 constraints the rates of changes between dN/dS values to be uniform (e.g., the rates of changes between negative and positive selection is constrained to be the same as the rate of change between neutrality and positive selection) while S2 allows for differents rates of change between the different classes of dN/dS values.

If you are using a 'switching' model, 'fitmodel' will output file with the following names: your_sequence_file_trees_w1, your_sequence_file_trees_w2, your_sequence_file_trees_w3 and your_sequence_file_trees_wbest.  The w1, w2 and w3 files give the estimated tree with probabilities of w1, w2, and w3 (three maximum likelihood dN/dS ratio estimates) calculated on each edge of the tree and for each site.  Hence, the first tree in one of these files reports the probabilities calculated at the first site of the alignment.  Instead of probabilities, the wbest file allows you to identify which of the tree dN/dS is the most probable on any give edge, at any given site.  A branch with label 0.0 means that w1 is the most probable class, 0.5 indicates the w2 is the most probable and 1.0 means that w3 has the highest posterior probability." (README.txt)


"Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line." (


MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.


LS-DYNA is a general purpose finite element code for simulating complex structural problems, specializing in nonlinear, transient dynamic problems using explicit integration. LS-DYNA is one of the codes developed at Livermore Software Technology Corporation (LSTC).


Jmol is a simple molecular visualization program. It can read many file formats and can write various formats. Animations of normal modes and simulations are implemented. Jmol is an OpenScience Java application.

Intel Compilers

The Intel compilers for both C/C++ and FORTRAN.

Availability and Restrictions

Intel Compiler is available on Glenn, Oakley and Ruby Clusters. The versions currently available at OSC are:


Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

  • if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
  • the top hits in a BLAST search are hypothetical sequences from genome projects.
  • your protein consists of several domains which are of different types.

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

HMMER is a very cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus available on a node. HMMER on OSC clusters are intended for those who need to run HMMER searches on large numbers of query sequences.


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