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<h1>Projects </h1>
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<ul>
 <li> The <a href="http://bioresearch.byu.edu/msa"><b>MSA</b></a> project provides FPGA and GPU accelerated multiple sequence alignment.
 <li> The <a href="http://bioresearch.byu.edu/psoda"><b>PSODA</b></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> <a href="http://bioresearch.byu.edu/mdsas"><b>MPSA2MDSA</b></a> was developed to create DNA alignment <a href="http://bioresearch.byu.edu/msdas/benchmarks.shtml">benchmarks</a> in order to test, rank, and improve current alignment algorithms. Thus far, the central focus on assessment of alignment applications has been on protein alignments; however, with a new "gold standard" of DNA alignments, it will be possible to better fill the need of good DNA alignment algorithms. <!--retrieves the best matching DNA sequence for a PROTEIN sequence query to estimate reverse translation.  It also applies the alignment from a multiple protein sequence alignment (MPSA) onto the corresponding hits and returns a multiple DNA sequence alignment (MDSA).  Using the later feature makes the first protein-coding DNA alignment benchmark possible.-->
<li><a href="http://bioresearch.byu.edu/lga"><b>Large Grain Alignment (LGA)</b></a> is a software package that iterates through phases of multiple sequence alignment, phylogeny searches and calculating substitution matrices to provide a large grain optimization alignment that provides more refined alignments then packages like ClustalW and overcomes limitations in current optimization alignment packages such as POY.
<li>  The Distributed Object Group Metacomputing Environment (<a href="http://bioresearch.byu.edu/dogma"><b>DOGMA</b></a>) project provides users with a distributed computing environment where computational science experiments can be executed on idle computers as well as clusters and supercomputers.
<li><a href="http://bioresearch.byu.edu/tcs"><b>TCS</b></a> is a Java computer program to estimate gene genealogies including multifurcations and/or reticulations (i.e. networks).
 <li> Many  <a href="http://bioresearch.byu.edu/data/">data files</a> have been assembled to test the software.      
 <li> The  <a href="http://bioresearch.byu.edu/DrugDockCapstone/">Drug Docking/Pathways </a> undergraduate research group information is also available here.
 <li> The <a href="http://bioresearch.byu.edu/jumpstart/">Jumpstart</a> phylogenetic search system allows you to reuse trees from previous searches in a current search.
 <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>
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Please send suggestions and questions to Quinn Snell (snell@cs.byu.edu)

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