Some extra files and figures:
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bestModel : the AA model chosen for each gene
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filter-lb-aaand filter-lb-fna2aa : the name of sequences filtered by long branch filtering
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FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.rates.csv : GTR+Alpha parameters for the 1st and 2nd codon positions for the FNA2AA-masked10sites-mask33taxa alignments
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pTpP_GC_box.pdf and names.csv : the GC content of species for all codon positions and the name of species used in pTpP_GC_box.pdf
- Drawn using plot.gc.R and data built using gc-stats.py
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taxon-occupancy.png : taxon occupancy
- Drawn using taxonOccupancyMap.R and data built using occupancy.sh
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annotations.csv : Mapping between 4-letter codes, species names, and a classification of species used to color figures in the paper
- Note: before the data release, for improved consistency with current literature, the following changes are made
- NPND: Changed
- Change all "BasalAngiosperms" to "ANAGrade"
- Change all "BasalEudicots" to "Eudicots"
- Note: before the data release, for improved consistency with current literature, the following changes are made