Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn

Teisher JK, McKain MR, Schaal BA, Kellogg EA

Date Published: June 23, 2017

DOI: http://dx.doi.org/10.5061/dryad.v7m05

 

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Title Unedited plastome alignment from MAFFT
Downloaded 4 times
Description 131 plastomes aligned using MAFFT by major region (LSC, SSC, IR) and then concatenated. No further modifications to alignment made.
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Title All Gaps Plastome Alignment
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Description 131 plastomes aligned using MAFFT by major region and then trimmed using the 'All Gaps' option in Gblocks.
Download allgaps_alignment.fsa (17.58 Mb)
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Title Half Gaps Plastome Alignment
Downloaded 10 times
Description 131 plastomes aligned using MAFFT by major regions and then trimmed using the 'Half Gaps' option in Gblocks.
Download halfgaps_alignment.fsa (14.43 Mb)
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Title No Gaps Plastome Alignment
Downloaded 4 times
Description 131 plastomes aligned using MAFFT by major regions and then trimmed using the 'No Gaps' option in Gblocks.
Download nogaps_alignment.fsa (11.22 Mb)
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Title Unedited ML Phylogeny
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Description RAxML phylogeny of plastome alignment not trimmed with Gblocks.
Download RAxML_bipartitions.plastomes_aligned2.fsa...ml.out (11.00 Kb)
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Title All Gaps ML Phylogeny
Downloaded 6 times
Description RAxML phylogeny of plastome alignment trimmed with the 'All Gaps' option in Gblocks
Download RAxML_bipartitions.allgaps_alignment.fsa.raxml.out (11.00 Kb)
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Title Half Gaps ML Phylogeny
Downloaded 7 times
Description RAxML phylogeny of plastome alignment trimmed with 'Half Gaps' option in Gblocks
Download RAxML_bipartitions.halfgaps_alignment.fsa...ml.out (11.00 Kb)
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Title No Gaps ML Phylogeny
Downloaded 5 times
Description RAxML phylogeny of plastome alignment trimmed with 'No Gaps' option in Gblocks
Download RAxML_bipartitions.nogaps_alignment.fsa.raxml.out (10.99 Kb)
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Title BEAST Input File
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Description Input XML file for each of 5 BEAST runs 100 million generations each.
Download BEAST_infile.xml (16.07 Mb)
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Title Bayesian All Gaps Phylogeny
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Description MrBayes phylogeny of plastome alignment trimmed with the 'All Gaps' option in Gblocks
Download MrBayesTree.tre (23.61 Kb)
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Title BEAST Run Logs
Downloaded 7 times
Description Combined logs from 5 runs of 100 million generations each in BEAST.
Download allgaps_mltree_combined.log.txt (27.53 Mb)
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Title BEAST Trees
Downloaded 4 times
Description Trees from 5 combined runs of 100 million generations each in BEAST
Download allgaps_mltree_combined.trees.txt (629.0 Mb)
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When using this data, please cite the original publication:

Teisher JK, McKain MR, Schaal BA, Kellogg EA (2017) Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn. Annals of Botany, online in advance of print. http://dx.doi.org/10.1093/aob/mcx058

Additionally, please cite the Dryad data package:

Teisher JK, McKain MR, Schaal BA, Kellogg EA (2017) Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v7m05
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