Molecular Ecology Resources.

Data and files

rubra_bt2_e2e.vcf.gz

VCF file of bases called against the Q. rubra reference using Bowtie 2 --end-to-end

rubra_bt2_local.vcf.gz

VCF file of bases called against the Q. rubra reference using Bowtie 2 --local

rubra_bwa.vcf.gz

VCF file of bases called against the Q. rubra reference using BWA

alba_bt2_e2e.vcf.gz

VCF file of bases called against the Q. alba reference using Bowtie 2 --end-to-end

alba_bt2_local.vcf.gz

VCF file of bases called against the Q. alba reference using Bowtie 2 --local

alba_bwa.vcf.gz

VCF file of bases called against the Q. alba reference using BWA

lobata_bt2_e2e.vcf.gz

VCF file of bases called against the Q. lobata reference using Bowtie 2 --end-to-end

lobata_bt2_local.vcf.gz

VCF file of bases called against the Q. lobata reference using Bowtie 2 --local

lobata_bwa.vcf.gz

VCF file of bases called against the Q. alba reference using BWA

mongolica_bt2_e2e.vcf.gz

VCF file of bases called against the Q. mongolica reference using Bowtie 2 --end-to-end

mongolica_bt2_local.vcf.gz

VCF file of bases called against the Q. mongolica reference using Bowtie 2 --local

mongolica_bwa.vcf.gz

VCF file of bases called against the Q. mongolica reference using BWA

ReferenceGenomeTest_v1.0.Rmd

this file is an R markdown file for analyzing the summary statistics and generating the figures for this manuscript
it reads the files in the inputFiles folder and exports the figures as pdfs to the outputFiles folder

inputFiles.zip

this is a folder with all the needed input files to run the ReferenceGenomeTest_v1.0.rmd file

alb_bt2-l.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus alba reference genome using Bowtie2 --local

alb_bt2_e2e.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus alba reference genome using Bowtie2 --end-to-end

alb_bwa.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus alba reference genome using bwa mem

lob_bt2-l.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus lobata reference genome using Bowtie2 --local

lob_bt2_e2e.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus lobata reference genome using Bowtie2 --end-to-end

lob_bwa.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus lobata reference genome using bwa mem

mong_bt2-l.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus mongolica reference genome using Bowtie2 --local

mong_bt2_e2e.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus mongolica reference genome using Bowtie2 --end-to-end

mong_bwa.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus mongolica reference genome using bwa mem

rub_bt2-l.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus rubra reference genome using Bowtie2 --local

rub_bt2_e2e.tre.treefile

tree from the concatenated matrix of samples mapped to the Quercus rubra reference genome using Bowtie2 --end-to-end

rub_bwa.tre.treefile_fixed

tree from the concatenated matrix of samples mapped to the Quercus rubra reference genome using bwa mem

Stats3.xlsx

an excel file with the statistics and data on each sample and reference genome. The "HetMissing" tab consists of heterozygosity and missing sites derived from vcftools output. The "AssemblyStats" tab consists of values data output from Bowtie2 or Samtools. The "BranchLengths" tab values were derived from the IQ-TREE2 topologies. Finally the "Samples" tab contains information also available on NCBI about the specimens.

taxa_trans_table.txt

a file with names for renaming species tree data

bt2_endtoend_script.txt

Script for processing reads post chloroplast filtering via Bowtie 2 --end-to-end to statistic calculation

bt2_local_script.txt

Script for processing reads post chloroplast filtering via Bowtie 2 --end-to-end to statistic calculation

bwa_script.txt

Script for processing reads post chloroplast filtering via Bowtie 2 --end-to-end to statistic calculation