Barrick Lab :: Software

<!-- Preferences start here

   * Set PAGETITLE = Barrick Lab :: Software

Preferences end here -->
---+ Barrick Lab :: Software

<font size="+1">&rarr; 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>
Barrick Lab > VjnbONNZ
Topic revision: r24 - 2025-09-17 - 00:47:39 - Main.TWikiGuest
Lab.SoftwareList moved from Lab.ToolList on 2023-09-20 - 15:41 by Main.JeffreyBarrick