Difference: SoftwareListAND238=68ANDoBgk=oBgk (1 vs. 24)

Revision 242025-09-16 - TWikiGuest

 
META TOPICPARENT name="WebHome" 
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  •  Set PAGETITLE = Barrick Lab :: Software

 


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Barrick Lab :: Software

→ Also check out our GitHub code repositories: https://github.com/barricklab

pLannotate (Plasmid Annotation)
Automated annotation of engineered DNA sequences and plasmids.
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
OSTIR (Open Source Translation Initiation Rates)
Prediction of translation initiation rates in E. coli and other bacteria.
CryptKeeper
Pipeline to predict burden from cryptic gene expression in E. coli.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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META TOPICMOVED by="JeffreyBarrick" date="1695224496" from="Lab.ToolList" to="Lab.SoftwareList"

Revision 232025-03-20 - CameronRoots

 
META TOPICPARENT name="WebHome" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Software

 


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Barrick Lab :: Software

→ Also check out our GitHub code repositories: https://github.com/barricklab

pLannotate (Plasmid Annotation)
Automated annotation of engineered DNA sequences and plasmids.
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
OSTIR (Open Source Translation Initiation Rates)
Prediction of translation initiation rates in E. coli and other bacteria.
Added:
>
>
CryptKeeper
Pipeline to predict burden from cryptic gene expression in E. coli.
 
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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META TOPICMOVED by="JeffreyBarrick" date="1695224496" from="Lab.ToolList" to="Lab.SoftwareList"

Revision 222024-05-18 - JeffreyBarrick

 
META TOPICPARENT name="WebHome" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Software

 


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Barrick Lab :: Software

Changed:
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<		→ Also check out our code repository: https://github.com/barricklab
>
>		→ Also check out our GitHub code repositories: https://github.com/barricklab
 
pLannotate (Plasmid Annotation)
Automated annotation of engineered DNA sequences and plasmids.
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
OSTIR (Open Source Translation Initiation Rates)
Prediction of translation initiation rates in E. coli and other bacteria.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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META TOPICMOVED by="JeffreyBarrick" date="1695224496" from="Lab.ToolList" to="Lab.SoftwareList"

Revision 212023-09-20 - JeffreyBarrick

 
META TOPICPARENT name="WebHome"
Changed:
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Barrick Lab :: Code

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Barrick Lab :: Software

  → Also check out our code repository: https://github.com/barricklab

pLannotate (Plasmid Annotation)
Automated annotation of engineered DNA sequences and plasmids.
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Added:
>
>
OSTIR (Open Source Translation Initiation Rates)
Prediction of translation initiation rates in E. coli and other bacteria.
 
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 202023-09-20 - JeffreyBarrick

 
META TOPICPARENT name="WebHome" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Sofware

 


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Barrick Lab :: Code

→ Also check out our code repository: https://github.com/barricklab

Added:
>
>
pLannotate (Plasmid Annotation)
Automated annotation of engineered DNA sequences and plasmids.
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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META FILEATTACHMENT attachment="pLannotate.png" attr="h" comment="" date="1695209055" name="pLannotate.png" path="pLannotate.png" size="7719" user="JeffreyBarrick" version="2"
 

Revision 192023-09-20 - JeffreyBarrick

 
META TOPICPARENT name="WebHome"

Barrick Lab :: Code

Changed:
<
<		→ Also check out our code repository: Code Github/BarrickLab
>
>		→ Also check out our code repository: https://github.com/barricklab
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 182020-07-08 - JeffreyBarrick

 
META TOPICPARENT name="WebHome" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Code

 


Preferences end here -->

Barrick Lab :: Code

→ Also check out our code repository: Code Github/BarrickLab

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
Deleted:
<
<

Getting started with Python for biology
Short guide and some good practices for getting started with Python for biology.
 

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Revision 172020-02-13 - MattMcGuffie

 
META TOPICPARENT name="WebHome" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Code

 


Preferences end here -->

Barrick Lab :: Code

→ Also check out our code repository: Code Github/BarrickLab

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
Added:
>
>

Getting started with Python for biology
Short guide and some good practices for getting started with Python for biology.
 

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Revision 162018-10-26 - JeffreyBarrick

Changed:
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<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Code

 


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Barrick Lab :: Code

→ Also check out our code repository: Code Github/BarrickLab

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 152018-10-25 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar"
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Barrick Lab :: Computational Tools

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>

Barrick Lab :: Code

 
Changed:
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<		→ Also check out Code Github/BarrickLab
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>		→ Also check out our code repository: Code Github/BarrickLab
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 142018-10-24 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Computational Tools

 


Preferences end here -->

Barrick Lab :: Computational Tools

Changed:
<
<		→ Also check out the BarrickLab on Github
>
>
Added:
>
>		→ Also check out Code Github/BarrickLab
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 132018-03-22 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Computational Tools

 


Preferences end here -->

Barrick Lab :: Computational Tools

Added:
>
>		→ Also check out the BarrickLab on Github
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 122015-03-21 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar" 
<-- Preferences start here

 
    

  •  Set PAGETITLE = Barrick Lab :: Computational Tools

 


Preferences end here -->

Barrick Lab :: Computational Tools

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Changed:
<
<
Evolutionary Failure Mode Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
>
>
Evolutionary Failure Mode (EFM) Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
 
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 112015-03-20 - JeffreyBarrick

 
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Barrick Lab :: Computational Tools

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Changed:
<
<
Evolutionary Failure Mode Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
>
>
Evolutionary Failure Mode Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
 
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 102015-03-06 - JeffreyBarrick

 
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Barrick Lab :: Computational Tools

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Added:
>
>
Evolutionary Failure Mode Calculator
Predict hypermutable sites in an engineered DNA sequence or microbial genome.
 
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 92012-05-01 - JeffreyBarrick

 
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Changed:
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Tools

>
>

Barrick Lab :: Computational Tools

 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.

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Revision 82011-01-30 - JeffreyBarrick

 
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Deleted:
<
<
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
 
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
Added:
>
>
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
 

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Revision 72011-01-20 - JeffreyBarrick

 
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<-- Preferences start here

 
    

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Tools

RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.

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Revision 62010-01-09 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar"

Tools

RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
Changed:
<
<
BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
>
>
Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
 
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.

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>
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Revision 52009-07-17 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar"

Tools

RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
Changed:
<
<
>
>
Added:
>
>
 
BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Deleted:
<
<
Marker Divergence Statistics
Analyze neutral marker divergence experiments to measure evolvability.
 
Changed:
<
<
Fluctuation Test Analysis (requires login)
Determine mutation rates from the results of a Luria-Delbrück fluctuation test.
>
>
Marker Divergence Experiments
Analyze neutral marker divergence experiments to measure evolvability.
 

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Revision 42009-03-10 - JeffreyBarrick

 
META TOPICPARENT name="WebLeftBar"

Tools

RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence Statistics
Analyze neutral marker divergence experiments to measure evolvability.
Added:
>
>
Fluctuation Test Analysis (requires login)
Determine mutation rates from the results of a Luria-Delbrück fluctuation test.
 

META FILEATTACHMENT attachment="MI_icon.gif" attr="h" comment="" date="1230387418" name="MI_icon.gif" path="MI_icon.gif" size="5144" stream="MI_icon.gif" user="Main.JeffreyBarrick" version="1"

Revision 32008-12-27 - JeffreyBarrick

 
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Tools

Changed:
<
<
>
>
Added:
>
>
RNA Structure Mutual Information
Predict interacting bases in an RNA alignment by estimating the phylogeny-corrected significance of mutual information between columns.
BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence Statistics
Analyze neutral marker divergence experiments to measure evolvability.

META FILEATTACHMENT attachment="MI_icon.gif" attr="h" comment="" date="1230387418" name="MI_icon.gif" path="MI_icon.gif" size="5144" stream="MI_icon.gif" user="Main.JeffreyBarrick" version="1"
 

Revision 22008-12-18 - JeffreyBarrick

 
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Tools

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  • RNA Structure Mutual Information
    Predict interacting bases in an RNA alignment by estimating the significance of phylogeny-corrected mutual information between columns.
 

Revision 12008-09-18 - JeffreyBarrick

 
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