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.
usage: blattabacteriaSetup.sh <path to file with *.fas files>
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)
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)
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/
usage: blattabacteriaSelectionSummary.sh
input: blattabacteriaGeneSummary.txt (from blattabacteriaGeneSummary.sh), output from selection tests
output: blattabacteriaSelectionSummary.txt
This is just a note about the parameters used to run the 16S tree; sequence alignment conversion was run separately (not in script)