Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

Rothfels CJ, Pryer KM, Li F

Date Published: August 4, 2016

DOI: http://dx.doi.org/10.5061/dryad.dj82k

 

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Title PURCvsSanger_trees
Downloaded 10 times
Description Contains two files (a nexus alignment and a tree file) of the comparison of the alleles inferred by PURC versus those from cloning and Sanger sequencing. See figure S1 in the paper.
Download PURCvsSanger_trees.zip (8.674 Kb)
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Title all_regimes_trees
Downloaded 9 times
Description For each of the four loci, contains a tree that includes all the alleles inferred by each of the six analysis regimes.
Download all_regimes_trees.zip (1.512 Mb)
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Title barcodes_pacbio
Downloaded 23 times
Description The 48 16-base barcodes designed by Pacific Biosciences.
Download barcodes_pacbio.xlsx (60.35 Kb)
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Title PURC_molecularlab_tracking
Downloaded 15 times
Description An example spreadsheet for sample tracking and library preparation (amplicon standardization, etc.)
Download PURC_molecularlab_tracking.xlsx (81.29 Kb)
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Title vouchertable_allruns
Downloaded 8 times
Description Voucher data for all three PacBio sequencing runs discussed in the manuscript.
Download vouchertable_allruns.xlsx (55.89 Kb)
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Title scripts_for_figures
Downloaded 11 times
Description Python and R scripts used to generate the figures.
Download scripts_for_figures.zip (12.06 Kb)
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Title extract_specific_accessions
Downloaded 7 times
Description This script finds the "allele" sequences for a given set of accessions, from all regimes and runs provided. It can be useful to look at the effect of different analysis regimes -- less overwhelming than trying to look at huge trees of all accessions at once. Alternatively, use the merge_allRegimes_and_align.sh bash script to get all the sequences, from all the accessions.
Download extract_specific_accessions.py (2.999 Kb)
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Title merge_allRegimes_and_align
Downloaded 6 times
Description Shell script to merge the inferred alleles from multiple analyses (ie, different analysis regimes) into a single alignment.
Download merge_allRegimes_and_align.sh (2.732 Kb)
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Title batch_run_purc
Downloaded 6 times
Description Example shell script to run purc_recluster.py multiple times, with different analyses settings.
Download batch_run_purc.sh (327 bytes)
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When using this data, please cite the original publication:

Rothfels CJ, Pryer KM, Li F (2016) Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytologist 213(1): 413-429. http://dx.doi.org/10.1111/nph.14111

Additionally, please cite the Dryad data package:

Rothfels CJ, Pryer KM, Li F (2016) Data from: Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.dj82k
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