Supporting data and information for Bacillus coat project, as in Hong Qin and Adam Driks, , "Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure", 2013, BMC Evolutionary Biology, 13:261 doi:10.1186/1471-2148-13-261.
URL: http://www.biomedcentral.com/1471-2148/13/261
All files are provided 'as is'.
Working folders are simply 'dumped' into this repository. Many links and path should be modified in order for the scripts to run.
Folder online.supplementary.files contain the supplementary files for Qin & Driks2013 coat.profile.for.submission.xlsx
Folder bacillus.species.tree contains the workfing files for 16s rDNA and 34 essential genes.
Folder bacillus.phylip.I3.1 contains the ortholog identification working files.
Folder tree.test contains the topology test using the highly conserved essential genes.
Folder compare.profiles is the working folder for orthologous profile analysis and heatmap generation.
Folder pairwise.matrix.omega.062310 is the working folder to perform the pairwise test and generate heatmaps.
File whole.genome.codemlLRT.tar contain the working folders for whole genome LRT test. The expanded directory is whole.genome.codemlLRT/ The original R working directory is ~/coat.protein07/ortholog.analysis/whole.genome.codeml.042109/R.Bha4sub4cereus
Folder key.data contains some key data used in the spore coat project.
Folder coatpaml contains the free omega runs that were excluded from the final submission to BMC Evolution.
File genomes.tar.gz contain the genomes used in the spore coat projects. Some additional genomes were also dumped here for future studies.
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