Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture

Teasdale LC, Köhler F, Murray KD, O'Hara T, Moussalli A

Date Published: May 24, 2016

DOI: http://dx.doi.org/10.5061/dryad.fn627

 

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Title 'Agalma best' alignments
Downloaded 7 times
Description The alignments representing a subset of the output of Agalma, run on 21 eupulmonate transcriptomes. This subset is the 546 orthologous clusters identified by Agalma, where each orthologous cluster was the only one produced from the respective homolog cluster and had sequences for at least 18 taxa. The alignments contain dummy sequences for missing taxa.
Download Agalma_best_alignments.tar.gz (756.6 Kb)
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Title 'Agalma equivalent' alignments
Downloaded 4 times
Description The alignments representing a subset of the output of Agalma, run on 21 eupulmonate transcriptomes. This subset is the 635 orthologous clusters identified by the automated pipeline Agalma, which correspond to the 500 nuclear single copy, orthologous genes identified by manual curation. The alignments contain dummy sequences for missing taxa.
Download Agalma_equivalent.tar.gz (653.8 Kb)
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Title Manual curation: 500 gene alignments
Downloaded 12 times
Description The alignments for 500 single copy, orthologous, nuclear genes across 21 representatives of the eupulmonates. Orthology was assessed through manual curation and gene tree assessment. Each alignment contains a mask, 'x' denotes regions that were masked out (i.e. remove from further analyses). The alignments contain dummy sequences for missing taxa.
Download Manual_curation_500_genes.tar.gz (2.825 Mb)
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Title Camaenidae alignment
Downloaded 6 times
Description The concatenated alignment of the 2,648 exons which were sequenced from representatives of the family Camaenidae using exon capture. This alignment was used to produce the camaenidae phylogeny presented in the paper.
Download all_exons_concat_cam.phy (10.78 Mb)
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Title Camaenidae_exon_capture_probe_set
Downloaded 5 times
Description This file contains the probes for the Camaenidae exon capture design. These probes target exons from 490 orthologous genes. The probes were designed for use with the Mycroarray Mybaits custom kit which consists of 120 bp RNA probes.
Download Sphaerospira-Austrochlotitis-120-60-v2_FINAL.fas (2.828 Mb)
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Title Manual_curation_500_genes_seperated_into_exons
Downloaded 8 times
Description This file contains the alignments for the 500 manually curated genes seperated out into alignments per exon based on the exon boundaries from the Lottia gigantea genome. These alignments contain the regions which are masked out in the gene alignments but the mask is not presented.
Download Manual_curation_500_genes_seperated_into_e...ar.gz (2.898 Mb)
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Title Trinity_assemblies
Downloaded 9 times
Description Transcriptome assemblies for 21 eupulmonate species. The transcriptomes were assembled using the program Trinity.
Download Trinity_assemblies.tar.gz (446.0 Mb)
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When using this data, please cite the original publication:

Teasdale LC, Köhler F, Murray KD, O'Hara T, Moussalli A (2016) Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture. Molecular Ecology Resources 16(5): 1107–1123. http://dx.doi.org/10.1111/1755-0998.12552

Additionally, please cite the Dryad data package:

Teasdale LC, Köhler F, Murray KD, O'Hara T, Moussalli A (2016) Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.fn627
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