<!-- Preferences start here * Set PAGETITLE = Barrick Lab :: Software Preferences end here --> ---+ Barrick Lab :: Software <font size="+1">→ Also check out our GitHub code repositories: [[https://github.com/barricklab][https://github.com/barricklab]]</font> <table cellpadding=4> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/pLannotate.png"></td> <td>[[http://plannotate.barricklab.org][pLannotate (Plasmid Annotation)]]<br>Automated annotation of engineered DNA sequences and plasmids.</td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/breseq_icon.gif"></td> <td>[[ToolsBacterialGenomeResequencing][Breseq (Bacterial Genome Resequencing)]]<br>Determine mutations in evolved bacteria from next-generation sequencing data.</td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/OSTIR.png"></td> <td> [[https://github.com/barricklab/ostir][OSTIR (Open Source Translation Initiation Rates)]]<br>Prediction of translation initiation rates in _E. coli_ and other bacteria.</td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/CryptKeeper.png"></td> <td> [[https://github.com/barricklab/cryptkeeper][CryptKeeper]]<br>Pipeline to predict burden from cryptic gene expression in _E. coli_.</td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/EFM_Calculator.png"></td> <td> [[http://barricklab.org/django/efm][Evolutionary Failure Mode (EFM) Calculator]]<br>Predict hypermutable sites in an engineered DNA sequence or microbial genome.</td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/marker_divergence_icon.gif"></td> <td> [[ToolsMarkerDivergence][Marker Divergence Experiments]]<br>Analyze neutral marker divergence experiments to measure evolvability. </td> </tr> <tr valign="top"> <td><img style="border-color: black; border-style: solid; border-width: 1px;" src="%ATTACHURL%/MI_icon.gif"></td> <td>[[ToolsRNAStructureMutualInformation][RNA Structure Mutual Information]]<br>Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns. </td> </tr> </table>
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Topic revision: r23 - 2025-03-20 - CameronRoots