https://github.com/k8hertweck/blattabacteria

Analyzing a set of genes using phylogenetics and tests for selection
https://github.com/k8hertweck/blattabacteria

bacteria hyphy

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Analyzing a set of genes using phylogenetics and tests for selection

• Host: GitHub
• URL: https://github.com/k8hertweck/blattabacteria
• Owner: k8hertweck
• Created: 2014-09-05T21:30:17.000Z (about 10 years ago)
• Default Branch: master
• Last Pushed: 2018-04-06T21:44:18.000Z (over 6 years ago)
• Last Synced: 2023-10-20T20:53:38.092Z (about 1 year ago)
• Topics: bacteria, hyphy
• Language: HTML
• Size: 32.5 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Blattabacteria 

==============

gene alignment, cleanup, tree building, and data summary

Authors: Austin Alleman and Kate Hertweck, The University of Texas at Tyler

Run scripts in order as they appears below. 

## Gene alignment, trimming, phylogeny building

usage: `blattabacteriaSetup.sh `

dependencies: 

* prinseq-lite (prinseq-lite.pl, installed as the executable prinseq-lite) http://prinseq.sourceforge.net

* translatorx (translatorx_vLocal.pl, installed as the executable translatorx) http://translatorx.co.uk

* trimal and readal http://trimal.cgenomics.org

* phyml http://atgc.lirmm.fr/phyml/

input: one unaligned fasta file for each gene (*.fas)

output: all included in `analysis/`, folder for each gene containing variety of files (including *.hyphy)

## Gene alignment and tree summaries

usage: `blattabacteriaGeneSummary.sh`

input: output from blattabacteriaSetup.sh, including readal.out and folder for each gene 

output: all included in `analysis/`, list of complete paths to each gene's *.hyphy file (blattabacteriaGenes.txt), table of gene summary stats (blattabacteriaGeneSummary.txt, tab delimited, column names: gene, alignLength, GC, BlatGC, FlavGC, treeLength)

## Selection tests in HYPHY

usage: `hyphy blattabacteriaQSD.bf > blattabacteriaQSD.out`

dependencies:

* HYPHY v2.2.1 (https://github.com/veg/hyphy)

Batch file wrappers:

* blattabacteriaQSD.bf

* blattabacteriaBranchSiteREL.bf

input: *.hyphy for each gene (fasta alignment with tree appended, located in gene directory), list of complete paths to each gene's *.hyphy file (blattabacteriaGenes.txt), *.bf file with complete paths to fileToExe and blattabacteriaGenes.txt modified to reflect your computer

output: all included in `analysis/`

	

## Selection test summaries

usage: `blattabacteriaSelectionSummary.sh`

input: blattabacteriaGeneSummary.txt (from blattabacteriaGeneSummary.sh), output from selection tests

output: blattabacteriaSelectionSummary.txt

## 16S tree

This is just a note about the parameters used to run the 16S tree; sequence alignment conversion was run separately (not in script)