Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ

Date Published: May 20, 2015

DOI: http://dx.doi.org/10.5061/dryad.s01kf

 

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Title Dataset_details
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Description A list of the alignment dataset files included in the Dryad repository, including the filtering thresholds used to generate each dataset.
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Title vcf_Ref-aligned_Aalcalica
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Description Directory containing the GATK output .vcf file from reference(O. niloticus)-aligned reads of A. alcalica. Directory contains 1 .vcf file and 1 index file.
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Title vcf_Ref-aligned_Agrahami
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Description Directory containing the GATK output .vcf file from reference-aligned reads of A. grahami. Directory contains 1 .vcf file and 1 index file.
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Title vcf_Ref-aligned_Alatilabris
Downloaded 2 times
Description Directory containing the GATK output .vcf file from reference-aligned reads of A. latilabris. Directory contains 1 .vcf file and 1 index file.
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Title vcf_Ref-aligned_Andalalani
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Description Directory containing the GATK output .vcf file from reference-aligned reads of A. ndalalani. Directory contains 1 .vcf file and 1 index file.
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Title vcf_Ref-aligned_Oamphimelas
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Description Directory containing the GATK output .vcf file from reference-aligned reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.
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Title vcf_de-novo_Aalcalica
Description Directory containing the GATK output .vcf file from denovo-assembled reads of A. alcalica. Directory contains 1 .vcf file and 1 index file.
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Title vcf_de-novo_Agrahami
Description Directory containing the GATK output .vcf file from denovo-assembled reads of A. grahami. Directory contains 1 .vcf file and 1 index file.
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Title vcf_de-novo_Alatilabris
Downloaded 3 times
Description Directory containing the GATK output .vcf file from denovo-assembled reads of A. latilabris. Directory contains 1 .vcf file and 1 index file.
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Title vcf_de-novo_Andalalani
Description Directory containing the GATK output .vcf file from denovo-assembled reads of A. ndalalani. Directory contains 1 .vcf file and 1 index file.
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Title vcf_de-novo_Oamphimelas
Downloaded 1 time
Description Directory containing the GATK output .vcf file from denovo-assembled reads of O. amphimelas. Directory contains 1 .vcf file and 1 index file.
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Title DatasetA_n92
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'.
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Title DatasetB_n25
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetC_n92
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetD_n92
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetE_n92
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetF_n48
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetG_n91
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetG_n91.gz (4.183 Mb)
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Title DatasetH_n91
Downloaded 2 times
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetJ_n91
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetK_n91
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetL_n91
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetL_n91.gz (4.358 Mb)
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Title DatasetM_n84
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetM_n84.gz (6.249 Mb)
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Title DatasetN_n84
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetP_n38
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetP_n38.gz (2.742 Mb)
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Title DatasetQ_n38
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetQ_n38.gz (40.28 Kb)
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Title DatasetR_n84
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetS_n16
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetT_n16
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetT_n16.gz (348.9 Kb)
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Title DatasetU_n16
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetV_n16
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
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Title DatasetW_n14
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetW_n14.gz (619.4 Kb)
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Title DatasetX_n24
Downloaded 1 time
Description Alignment of sequence data, filtered according to the parameters listed in the file 'Dataset_details.csv'
Download DatasetX_n24.gz (31.19 Kb)
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Title Output_tree_files
Description Tree files from ML and SNAPP analysis, including the results presented in the following manuscript figures: 2, S3, S4, S5.
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When using this data, please cite the original publication:

Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ (2015) High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Molecular Ecology 24(13): 3421-3440. http://dx.doi.org/10.1111/mec.13247

Additionally, please cite the Dryad data package:

Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ (2015) Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.s01kf
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