Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J

Date Published: November 13, 2015

DOI: http://dx.doi.org/10.5061/dryad.dn08t

 

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Title ASTRAL_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq
Downloaded 9 times
Description ASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
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Title ASTRAL_speciesTree_fromRAxMLGeneTrees_OxalisHybSeq
Downloaded 6 times
Description ASTRAL species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
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Title MP-EST_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq
Downloaded 5 times
Description MP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
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Title MP-EST_speciesTree_fromRAxMLGeneTrees_OxalisHybSeq
Downloaded 4 times
Description MP-EST species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
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Title STAR_speciesTree_fromMrBayesGeneTrees_OxalisHybSeq
Downloaded 8 times
Description STAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
Download STAR_speciesTree_fromMrBayesGeneTrees_Oxa...eq.nwk (1.239 Kb)
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Title STAR_bootstrappedSpeciesTree_fromRAxMLGeneTrees_OxalisHybSeq
Downloaded 11 times
Description Bootstrapped STAR species tree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
Download STAR_bootstrappedSpeciesTree_fromRAxMLGen...eq.nwk (1.377 Kb)
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Title MRP_supertree_fromMrBayesGeneTrees_OxalisHybSeq
Downloaded 10 times
Description MRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with Bayesian inference). Oxalis corniculata was used as outgroup.
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Title MRP_supertree_fromRAxMLGeneTrees_OxalisHybSeq
Downloaded 7 times
Description MRP supertree from 727 low-copy nuclear gene trees of 25 southern African Oxalis accessions (gene tree estimation with maximum likelihood). Oxalis corniculata was used as outgroup.
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Title concatenatedLCNloci_bootstrapped_RAxML_OxalisHybSeq
Downloaded 7 times
Description Bootstrapped maximum likelihood tree based on concatenation of 727 low-copy nuclear genes of 25 southern African Oxalis accessions. Oxalis corniculata was used as outgroup.
Download concatenatedLCNloci_bootstrapped_RAxML_Ox...eq.nwk (1.85 Kb)
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Title MrBayesGeneTrees_OxalisHybSeq
Downloaded 7 times
Description Bayesian inference gene trees of 727 low-copy nuclear genes of 25 southern African Oxalis accessions and Oxalis corniculata.
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Title RAxMLGeneTrees_OxalisHybSeq
Downloaded 7 times
Description Maximum likelihood gene trees of 727 low-copy nuclear genes of southern African Oxalis accessions and Oxalis corniculata.
Download RAxMLGeneTrees_OxalisHybSeq.nwk (464.5 Kb)
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Title plastome_MrBayesMajorityRuleConsensusTree_OxalisHybSeq
Downloaded 7 times
Description Bayesian inference majority rule consensus tree of the plastome of 25 southern African Oxalis accessions and Oxalis latifolia. The alignment was partitioned into protein-, tRNA-, and rRNA-coding as well as intron/spacer (i.e., non-coding) regions.
Download plastome_MrBayesMajorityRuleConsensusTree...eq.tre (4.509 Kb)
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Title nrDNAcistron_MrBayesMajorityRuleConsensusTree_OxalisHybSeq
Downloaded 5 times
Description Bayesian inference majority rule consensus tree of the nrDNA cistron of 25 southern African Oxalis accessions and Oxalis corniculata. The nrDNA alignment was partitioned into 18S, ITS1, 5.8S, ITS2 and 26S.
Download nrDNAcistron_MrBayesMajorityRuleConsensus...eq.tre (4.185 Kb)
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Title geneious_deNovoAssembly_OxalisHybSeq
Downloaded 6 times
Description FASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač)
Download geneious_deNovoAssembly_OxalisHybSeq.fasta (9.139 Mb)
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Title probeSequences_OxalisHybSeq
Downloaded 9 times
Description Final low-copy nuclear probe sequences (output of step 11 of Sondovač)
Download probeSequences_OxalisHybSeq.fasta (1.273 Mb)
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Title Assembly_LCNloci_OxalisHybSeq
Downloaded 14 times
Description Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
Download Assembly_LCNloci_OxalisHybSeq.zip (244.0 Mb)
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Title Assembly_plastome_OxalisHybSeq
Downloaded 13 times
Description Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
Download Assembly_plastome_OxalisHybSeq.zip (101.3 Mb)
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Title Assembly_nrDNAcistron_OxalisHybSeq
Downloaded 13 times
Description Alignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)
Download Assembly_nrDNAcistron_OxalisHybSeq.zip (15.14 Mb)
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Title alignment_concatenatedLCNloci_OxalisHybSeq
Downloaded 5 times
Description Alignment of 727 concatenated low-copy nuclear genes of 25 southern African Oxalis accessions
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Title alignment_plastome_OxalisHybSeq
Downloaded 8 times
Description Alignment of the plastome of 25 southern African Oxalis accessions
Download alignment_plastome_OxalisHybSeq.fas (3.240 Mb)
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Title alignment_nrDNAcistron_OxalisHybSeq
Downloaded 7 times
Description Alignment of the nrDNA cistron of 25 southern African Oxalis accessions
Download alignment_nrDNAcistron_OxalisHybSeq.fas (144.9 Kb)
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Title RawReads_OxalisHybSeq
Downloaded 35 times
Description For a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawReads_OxalisHybSeq.doc"
Download RawReads_OxalisHybSeq.gz (5.932 Gb)
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When using this data, please cite the original publication:

Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J (2016) Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae). Molecular Ecology Resources 16(5): 1124–1135. http://dx.doi.org/10.1111/1755-0998.12487

Additionally, please cite the Dryad data package:

Schmickl R, Liston A, Zeisek V, Oberlander K, Weitemier K, Straub SCK, Cronn RC, Dreyer LL, Suda J (2015) Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.dn08t
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