Data from: Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences

Huang H, Knowles LL

Date Published: June 27, 2014

DOI: http://dx.doi.org/10.5061/dryad.jf361

 

Files in this package

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Title speciestree
Downloaded 18 times
Description 20 species tree simulated under Yule model using Mesquite
Download speciestree.nex (7.539 Kb)
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Title ms
Downloaded 22 times
Description Perl script to simulate coalescent genealogies for given species tree
Download ms.pl (5.185 Kb)
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Title seqgene_paramter
Downloaded 16 times
Description short R script to generate random mutation rates (as the theta for simulating dna sequences ) from a log normal distribution
Download seqgene_paramter.R (192 bytes)
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Title seqgen parameters
Downloaded 18 times
Description the result from seqgene_paramter.R-- the mutation rates used in simulating sequences
Download seqge.parameter (887.3 Kb)
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Title seq-gen
Downloaded 29 times
Description Perl script to simulate sequences given genealogies and mutation rate (as theta)
Download seq-gen.pl (2.656 Kb)
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Title infomissing
Downloaded 15 times
Description a Perl script to filter out sequences with mutations at enzyme cutting sites
Download infomissing.pl (1.679 Kb)
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Title coverage
Downloaded 11 times
Description a Perl script for filtering out sequences with no read (coverage draw from a poisson distribution)
Download coverage.pl (2.907 Kb)
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Title cluster
Downloaded 20 times
Description a Perl script for generating post-sequencing missing data
Download cluster.pl (2.922 Kb)
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Title lociind
Downloaded 14 times
Description a perl script for summarizing the number of individuals for each locus (output in a txt file)
Download lociind.pl (1.235 Kb)
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Title counts
Downloaded 13 times
Description a Perl script for counting the number loci at different tolerance levels (output a txt file)
Download counts.pl (1.687 Kb)
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Title phyliprand
Downloaded 12 times
Description a Perl script for generating phylip formatted sequence files with two tolerance levels (as the number of minimal individuals)--one for specifying the number of loci, and one for specifying the mutation-rate spectrum
Download phyliprand.pl (3.616 Kb)
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Title monosp_dryad
Downloaded 22 times
Description R code for calculating the number of monophyletic clades on estimated gene tree
Download monosp_dryad.R (8.837 Kb)
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Title mindis
Downloaded 81 times
Description R script for shallowest divergenece species tree estimation
Download mindis.R (5.241 Kb)
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Title treedist
Downloaded 14 times
Description R script for calculating RF distance
Download treedist.R (7.5 Kb)
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Title raxml
Downloaded 11 times
Description run raxml
Download raxml.pl (1.541 Kb)
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Title Genealogy.tar
Downloaded 6 times
Description Simulated genalogies
Download Genealogy.tar.gz (196.1 Mb)
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Title CompleteSequenceData.tar
Downloaded 9 times
Description Simulated complete sequence data
Download CompleteSequenceData.tar.gz (182.7 Mb)
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Title CuttingMissing.tar
Downloaded 8 times
Description remaining sequences after filtering out sequences with mutations at enzyme cutting sites
Download CuttingMissing.tar.gz (129.2 Mb)
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Title CoverageMissing.tar
Downloaded 7 times
Description remaining data after filtering sequences with zero read, mean coverage set to 5x
Download CoverageMissing.tar.gz (164.8 Mb)
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Title CoverageOneMissing.tar
Downloaded 9 times
Description Remaining data after filtering out sequences with no read, mean coverage set to 1x
Download CoverageOneMissing.tar.gz (108.1 Mb)
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Title DataProcessingMissing.tar
Downloaded 6 times
Description remaining data after data processing steps, mean coverage 5x
Download DataProcessingMissing.tar.gz (122.9 Mb)
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Title DataProcessingOneMissing.tar
Downloaded 8 times
Description Remaining sequences after data processing step, mean coverage 1x
Download DataProcessingOneMissing.tar.gz (46.11 Mb)
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Title Dryadfilelist
Downloaded 16 times
Description File list and explanations
Download Dryadfilelist.txt (1.946 Kb)
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When using this data, please cite the original publication:

Huang H, Knowles LL (2014) Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Systematic Biology 65(3): 357-365. http://dx.doi.org/10.1093/sysbio/syu046

Additionally, please cite the Dryad data package:

Huang H, Knowles LL (2014) Data from: Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jf361
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