Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens

Spribille T, Tuovinen V, Resl P, Vanderpool D, Wolinski H, Aime MC, Schneider K, Stabentheiner E, Toome-Heller M, Thor G, Mayrhofer H, Johannesson H, McCutcheon JP

Date Published: August 2, 2016

DOI: http://dx.doi.org/10.5061/dryad.7qv72

 

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Title readme_scripts
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Description File describing the scripts included in this Dryad accession
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Title 01_count_SNPs_extended_version
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Description python script for counting SNPs
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Title 001_get_longest_transcript
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Description Python script for identifying longest transcripts
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Title 002_get_orfs_from_longest_seqs
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Description Python script for retrieving open reading frames from longest Trinity transcripts per component
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Title 02_merge_SNP_counts_w_lens
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Description Python script for performing merge of counts and lengths files
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Title 03_collapse_to_longest
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Description Python script for collapsing a set of transcripts to only the longest single splicing isoforms
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Title 003_get_best_evalues
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Description Python script for identifying the best blast e-values from a set of multiple blast results for a single transcript
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Title 004_add_taxa_to_abundance_table
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Description Python script to link taxon lineage information with an eXpress gene abundance output
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Title 04_add_taxon_to_SNPs
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Description Python script to annotate a transcript SNP table with taxon information from a blast result
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Title 05_collapse_to_best_evalue
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Description Python script to identify the blast result with the highest e-value from a set of multiple blast results on a single contig (different input data formats)
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Title 06_filter_vcf_for_targets
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Description Python script to strip out pre-identified targets from a variant call format file
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Title all_master_work_wSNPs
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Description An Excel spreadsheet showing all blast-annotated non-redundant transcripts with eXpress abundance data for each transcriptome and a final column showing which of these transcripts contain passing SNPs based on analyses described in the paper
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Title edgeR_mar2016
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Description R script used to identify differentially expressed genes between samples coded as Bryoria tortuosa and those coded as B. fremontii
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Title 39Dikary.349loci.CONCAT
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Description Protein fasta file for 349 loci used in phylogenomic analysis; see readme_align file
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Title 39Dikary.58loci.CONCAT
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Description Phylip file used for dating the phylogenomic tree of fungi
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Title A_ITS_all_red_mafft_replaced_cut
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Description see readme_align.txt
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Title A_ITS_all_red_mafft_replaced
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Description see readme_align.txt
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Title B_SSU_all_red_mafft_replaced_cut
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Description see readme_align.txt
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Title B_SSU_all_red_mafft_replaced
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Description see readme_align.txt
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Title C_LSU_all_red_mafft_replaced_cut
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Description see readme_align.txt
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Title C_LSU_all_red_mafft_replaced
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Description see readme_align.txt
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Title concat_cut
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Description see readme_align.txt
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Title Fig2A_FigS3A_Dikary39.NOcal_lnrootP_sample.chronogram
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Description Tree file underlying Fig2A. See readme_align.txt
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Title Fig2B_Fig3B_RAxML_bipartitions.cystos_130316_correct_names
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Description Tree file underlying Fig. 2B. See readme_align.txt
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Title FigS4_Dikary39.1calConcat_lnrootP_sample.chronogram
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Description Tree file underlying Fig. S4. See readme_align.txt
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Title FigS5_Dikary39.4cal_lnrootP_sample.chronogram
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Description Tree file underlying Fig. S5. See readme_align.txt
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Title FigS12_RAxML_bipartitions.cystosITS_120316_correct_names.test
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Description Tree file underlying Fig. S12. See readme_align.txt
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Title FigS13_RAxML_bipartitions.cystosLSU_120316_correct_names.test
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Description Tree file underlying Fig. S13. See readme_align.txt
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Title FigS14_RAxML_bipartitions.cystosSSU_120316_correct_names.test
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Description Tree file underlying Fig. S14. See readme_align.txt
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Title MLSuperMatrix.wIC.75BTSP.CONSENSE
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Description Alignment used for internode uncertainty analysis
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Title SuperTREE_IC.MRE.39tax.58loci.CON75percent
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Description Tree file underlying internode certainty analysis
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Title readme_align
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Description ReadMe file for all alignments and tree files associated with this submission.
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When using this data, please cite the original publication:

Spribille T, Tuovinen V, Resl P, Vanderpool D, Wolinski H, Aime MC, Schneider K, Stabentheiner E, Toome-Heller M, Thor G, Mayrhofer H, Johannesson H, McCutcheon JP (2016) Basidiomycete yeasts in the cortex of ascomycete macrolichens. Science 353(6298): 488-492. http://dx.doi.org/10.1126/science.aaf8287

Additionally, please cite the Dryad data package:

Spribille T, Tuovinen V, Resl P, Vanderpool D, Wolinski H, Aime MC, Schneider K, Stabentheiner E, Toome-Heller M, Thor G, Mayrhofer H, Johannesson H, McCutcheon JP (2016) Data from: Basidiomycete yeasts in the cortex of ascomycete macrolichens. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7qv72
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