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

ASTRAL_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqASTRAL 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.ASTRAL_speciesTree_fromRAxMLGeneTrees_OxalisHybSeqASTRAL 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.MP-EST_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqMP-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.MP-EST_speciesTree_fromRAxMLGeneTrees_OxalisHybSeqMP-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.STAR_speciesTree_fromMrBayesGeneTrees_OxalisHybSeqSTAR 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.STAR_bootstrappedSpeciesTree_fromRAxMLGeneTrees_OxalisHybSeqBootstrapped 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.MRP_supertree_fromMrBayesGeneTrees_OxalisHybSeqMRP 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.MRP_supertree_fromRAxMLGeneTrees_OxalisHybSeqMRP 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.concatenatedLCNloci_bootstrapped_RAxML_OxalisHybSeqBootstrapped maximum likelihood tree based on concatenation of 727 low-copy nuclear genes of 25 southern African Oxalis accessions. Oxalis corniculata was used as outgroup.MrBayesGeneTrees_OxalisHybSeqBayesian inference gene trees of 727 low-copy nuclear genes of 25 southern African Oxalis accessions and Oxalis corniculata.RAxMLGeneTrees_OxalisHybSeqMaximum likelihood gene trees of 727 low-copy nuclear genes of southern African Oxalis accessions and Oxalis corniculata.plastome_MrBayesMajorityRuleConsensusTree_OxalisHybSeqBayesian 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.nrDNAcistron_MrBayesMajorityRuleConsensusTree_OxalisHybSeqBayesian 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.geneious_deNovoAssembly_OxalisHybSeqFASTA output of the de novo assembly of the transcript or genome skim BLAT hits to larger contigs (step 7 of Sondovač)probeSequences_OxalisHybSeqFinal low-copy nuclear probe sequences (output of step 11 of Sondovač)Assembly_LCNloci_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)Assembly_plastome_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)Assembly_nrDNAcistron_OxalisHybSeqAlignreads ACE assembly files of 24 southern African Oxalis accessions (Hyb-Seq) and one genome skim accession (J12)alignment_concatenatedLCNloci_OxalisHybSeqAlignment of 727 concatenated low-copy nuclear genes of 25 southern African Oxalis accessionsalignment_plastome_OxalisHybSeqAlignment of the plastome of 25 southern African Oxalis accessionsalignment_nrDNAcistron_OxalisHybSeqAlignment of the nrDNA cistron of 25 southern African Oxalis accessionsRawReads_OxalisHybSeqFor a description of the contents of "RawReads_OxalisHybSeq.gz" please see "RawReads_OxalisHybSeq.doc"