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<title>CSL</title>

<h1>Computational Science Laboratory</h1>
	The Computational Science Laboratory investigates new algorithms for solving problems in computational biology, computational chemistry and computational physics. Emphasis is placed on finding efficient algorithms that can be run on parallel computers.
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<h1> Resources </h1>
The Laboratory currently uses computational resources from the <a href="http://marylou.byu.edu/"> Fulton Supercomputing Center </a> as well as 600-800 idle desktop nodes across the BYU campus that are managed by the <a href="dogma/"> DOGMA </a> system.
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<h1> Software </h1>
Several software packages have been developed by members of the laboratory including:
<ul>
<li> <a href="/gnumap">GNUMAP</a> maps reads from next-generation sequencers to genomic data.
<li> <a href="/dogma">DOGMA</a> uses idle computers as well as clusters and supercomputers for distributed scientific computing.
 <li> The <a href="/psoda">PSODA</a> project provides a phylogenetic search tool that reads the same data file format as <a href="http://paup.csit.fsu.edu/">PAUP*</a>.
<li> Members of the laboratory collaborate with the Department of 
Integrative Biology to develop software to analyze biochemical 
properties when performing alignment or phylogeny search.  
This <a href="http://inbio.byu.edu/faculty/dam83/cdm"> software </a> 
performs a detailed analysis of selection on amino acid properties using user-defined phylogenetic trees.
 <li> The <a href="/tcs/"> TCS </a> project estimates gene genealogies including multifurcations and/or reticulations (i.e. networks). The network estimation implemented in TCS is also known as Statistical Parsimony, which is described in Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. 
 <li> The <a href="/scaffoldscaffolder/">ScaffoldScaffolder</a> project is for haplotype-aware scaffolding of contigs. It also includes modules for solving the Contig Orientation Problem.
</ul>

<h1> Funding </h1>
The laboratory is currently supported by an <a href="proposal.html"> NSF grant </a> to investigate hexapod phylogeny.  
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