Data from: Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment

Stephens JD, Rogers WL, Mason CM, Donovan LA, Malmberg RL

Date Published: June 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.4n28n

 

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Title Helianthus chloroplast
Downloaded 7 times
Description This file contains the aligned 96789bp chloroplast sequences from 103 accessions across 37 diploid Helianthus species/subspecies and the outgroup Phoebanthus tenuifolius.
Download Helianthus_chloroplast.fasta (10.96 Mb)
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Title Chloroplast_tree
Downloaded 7 times
Description The cholorplast tree in newick format containing 103 accessions.
Download Chloroplast_tree.tre (3.112 Kb)
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Title Helianthus_Species_branchlengths
Downloaded 13 times
Description This is the file that contains the branch lengths as estimated with RAxML and using the MP-EST topology for the diploid Helianthus species.
Download Helianthus_Species_branchlengths.nwk (2.248 Kb)
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Title Helianthus_population_branchlengths
Downloaded 4 times
Description This file contains the population level tree with branch lengths estimated by RAxML with the fixed MP-EST topology for the diploid Helianthus species.
Download Helianthus_population_branchlengths.nwk (4.567 Kb)
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Title MPEST_Speciestree
Downloaded 14 times
Description The MP-EST species tree in newick format for 103 accessions estimated from 170 genes.
Download MPEST_Speciestree.tre (1.637 Kb)
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Title MPEST_population
Downloaded 8 times
Description The MP-EST population level tree estimated using 170 genes across 103 accessions.
Download MPEST_population.tre (3.296 Kb)
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Title Accession_tree
Downloaded 4 times
Description MP-EST accession tree estimated from 170 genes and 103 accessions
Download Accession_tree.tre (4.343 Kb)
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Title Concatenation_tree
Downloaded 8 times
Description Concatenation tree estimated from RAxML (106,862bp) across 103 accessions of diploid Helianthus.
Download Concatenation_tree.tre (3.474 Kb)
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Title Helianthus_concatenated_nDNA
Downloaded 6 times
Description This file contains the aligned 106862bp concatenated nDNA sequences from 103 accessions across 37 diploid Helianthus species/subspecies and the outgroup Phoebanthus tenuifolius.
Download Helianthus_concated_nDNA.fasta (11.00 Mb)
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Title Helianthus_fasta_files
Downloaded 40 times
Description This is the zip folder containing the fasta files for 170 genes across 103 diploid Helianthus species. The fasta files have been aligned and trimmed with gblocks.
Download Helianthus_fasta.zip (503.6 Kb)
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Title bootstrap_genetrees
Downloaded 37 times
Description The zip file contains all the bootstrap gene files. There are 170 files (one for each gene) with 500 bootstrapped gene trees within each file. These were all estimated from RAxML and used in MP-EST to estimate the species tree.
Download bootstrap_genetrees.zip (12.21 Mb)
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When using this data, please cite the original publication:

Stephens JD, Rogers WL, Mason CM, Donovan LA, Malmberg RL (2015) Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment. American Journal of Botany 102(6): 910-920. http://dx.doi.org/10.3732/ajb.1500031

Additionally, please cite the Dryad data package:

Stephens JD, Rogers WL, Mason CM, Donovan LA, Malmberg RL (2015) Data from: Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4n28n
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