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It implements methods using probabilistic models called profile hidden Markov models (profile HMMs)./wsu/apps/modules/hmmer-3.1b2 IBM ILOG CPLEX Optimizer Optimization software package for solving integer, linear, and quadratic programming problems. page_id=517 Bootstrapping based software package that can be used to perform differential gene expression analysis for RNA-Seq data both with and without replicates.

/wsu/apps/gnu-4.4.7/abinit/abinit-7.6.4 /wsu/apps/intel-14.0.2/abinit/abinit-7.6.4 AMBER Programs that allow users to carry out molecular dynamics simulations, particularly on biomoleculars.

/wsu/apps/modules/openmpi-1.8.4 /wsu/apps/modules/openmpi-1.8.8 Perl Practical Extraction and Report Language (Perl) is a a programming language useful for various tasks, such as bioinformatics, system administration, finance, network programming, web development.

/wsu/apps/gnu-4.4.7/perl/perl-5.20.1/ /wsu/apps/gnu-4.7.2/perl/perl-5.20.1 PGI Compilers, Fortran, C and C for 64-bit AMD64 and 64-bit IA32/EM64T processor-based Linux systems. F77 and F90 routines are still provided by the PGI compiler suite.

/wsu/apps/pre-compiled/monolix/monolix-432s/bin/MUSIC (MUlti Scale Enr Ichment Calling) for identifying enriched region at multiple length scales using data from Ch IP-Seq experiments.

/wsu/apps/gnu-4.4.7/music/music-2015-04-17/bin/MUSIC MVAPICH Libraries for message passing optimized for Infiniband.

GD can read and write many different image formats.

GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly./wsu/apps/pre-compiled/cufflinks/cufflinks-2.2.1 Fast ML Bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences./wsu/apps/gnu-4.7.2/Fast ML/Fast ML.v3.1 Fast Tree Software for inferring approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences./wsu/apps/gnu-4.7.2/Fast Tree/Fast Tree-2.1.7 FFTW Library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, of both real and complex data, and of even/odd data such as the discrete cosine/sine transforms or DCT/DST./wsu/apps/gnu-4.4.7/fftw/fftw2-2.1.5 /wsu/apps/gnu-4.4.7/fftw/fftw3-3.3.4 /wsu/apps/pgi-14.6/fftw/fftw-2.1.5 /wsu/apps/pgi-14.6/fftw/fftw-3.3.4-openmp Gaussian for electronic structure./wsu/apps/pre-compiled/namd/NAMD_2.11b1_Linux-x86_64-multicore /wsu/apps/pre-compiled/namd/NAMD_2.11b1_Linux-x86_64-TCP /wsu/apps/pre-compiled/namd/NAMD_2.11b1_Linux-x86_64-multicore-CUDA /wsu/apps/pre-compiled/namd/NAMD_2.11_Linux-x86_64-multicore /wsu/apps/pre-compiled/namd/NAMD_2.11_Linux-x86_64-TCP Open FOAM The Open Field Operation and Manipulation CFD toolbox.