Difference: SoftwareList (1 vs. 23)

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.

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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 FILEATTACHMENT	attachment="pLannotate.png" attr="h" comment="" date="1695209055" name="pLannotate.png" path="pLannotate.png" size="7719" user="JeffreyBarrick" version="2"
META FILEATTACHMENT	attachment="OSTIR.png" attr="h" comment="" date="1695224111" name="OSTIR.png" path="OSTIR.png" size="7047" user="JeffreyBarrick" version="2"

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META FILEATTACHMENT	attachment="CryptKeeper.png" attr="h" comment="CryptKeeper Logo" date="1742499963" name="CryptKeeper.png" path="CryptKeeper.png" size="5161" user="CameronRoots" version="1"

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

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

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→ 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.

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"
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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"

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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.

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"
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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"

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META FILEATTACHMENT	attachment="OSTIR.png" attr="h" comment="" date="1695224111" name="OSTIR.png" path="OSTIR.png" size="7047" user="JeffreyBarrick" version="2"
META TOPICMOVED	by="JeffreyBarrick" date="1695224496" from="Lab.ToolList" to="Lab.SoftwareList"

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

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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.

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"
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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

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→ Also check out our code repository:

Github/BarrickLab

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→ 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.

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"
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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: 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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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
 

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Barrick Lab :: Code

→ Also check out our code repository: 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

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META TOPICPARENT	name="WebHome"

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Code
 

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Barrick Lab :: Code

→ Also check out our code repository: 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.

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"
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META FILEATTACHMENT	attachment="EFM_Calculator.png" attr="h" comment="" date="1425609310" name="EFM_Calculator.png" path="EFM_Calculator.png" size="12168" stream="EFM_Calculator.png" tmpFilename="/usr/tmp/CGItemp32006" user="JeffreyBarrick" version="1"

Revision 152018-10-25 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

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Barrick Lab :: Computational Tools

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Barrick Lab :: Code

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→ Also check out

Github/BarrickLab

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→ Also check out our code repository:

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.

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"
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Revision 142018-10-24 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

<-- Preferences start here
 

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Barrick Lab :: Computational Tools

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→ Also check out the BarrickLab on Github

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Added:

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→ Also check out

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.

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"
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Revision 132018-03-22 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Computational Tools
 

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Barrick Lab :: Computational Tools

Added:

>
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→ 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.

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"
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Revision 122015-03-21 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Computational Tools
 

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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 (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.

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"
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Revision 112015-03-20 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

<-- Preferences start here
 

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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

META TOPICPARENT	name="WebLeftBar"

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Barrick Lab :: Computational Tools

Breseq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.

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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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Tools

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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

META TOPICPARENT	name="WebLeftBar"

<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Computational Tools
 

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Tools

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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.

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"
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Revision 72011-01-20 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

Added:

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<-- Preferences start here
 

 Set PAGETITLE = Barrick Lab :: Computational Tools
 

Preferences end here -->

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:

<
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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.

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"

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META FILEATTACHMENT	attachment="marker_divergence_icon.gif" attr="h" comment="" date="1247863094" name="marker_divergence_icon.gif" path="marker_divergence_icon.gif" size="4286" stream="marker_divergence_icon.gif" tmpFilename="/usr/tmp/CGItemp25409" user="JeffreyBarrick" version="2"

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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:

<
<

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>

Added:

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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:

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Fluctuation Test Analysis (requires login)
Determine mutation rates from the results of a Luria-Delbrück fluctuation test.

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Marker Divergence Experiments
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"

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META FILEATTACHMENT	attachment="marker_divergence_icon.gif" attr="h" comment="" date="1247863094" name="marker_divergence_icon.gif" path="marker_divergence_icon.gif" size="4286" stream="marker_divergence_icon.gif" tmpFilename="/usr/tmp/CGItemp25409" user="JeffreyBarrick" version="2"
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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

META TOPICPARENT	name="WebLeftBar"

Tools

Changed:

<
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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.
BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence
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.
	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

META TOPICPARENT	name="WebLeftBar"

Tools

Changed:

<
<

>
>

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

BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence
Analyze neutral marker divergence experiments to measure evolvability.

Revision 12008-09-18 - JeffreyBarrick

META TOPICPARENT	name="WebLeftBar"

Tools

BreSeq (Bacterial Genome Resequencing)
Determine mutations in evolved bacteria from next-generation sequencing data.
Marker Divergence
Analyze neutral marker divergence experiments to measure evolvability.

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