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INDEX_1_BARCODES.txt (0.13 kB)

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INDEX_2_BARCODES.txt (0.13 kB)

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INDEX_3_BARCODES.txt (0.13 kB)

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INDEX_4_BARCODES.txt (0.12 kB)

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Index_1_S1_R1_001.fastq.gz (5.04 GB)

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Index_1_S1_R2_001.fastq.gz (5.33 GB)

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Index_2_S2_R1_001.fastq.gz (3.86 GB)

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Index_2_S2_R2_001.fastq.gz (4.09 GB)

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Index_3_S3_R1_001.fastq.gz (3.94 GB)

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Index_3_S3_R2_001.fastq.gz (4.14 GB)

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Index_4_S4_R1_001.fastq.gz (1.36 GB)

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Index_4_S4_R2_001.fastq.gz (1.41 GB)

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filtered_mac2_minq30_missing50_minDP2.varsites.phy (4.56 MB)

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missing_0_minDP2mac2minq30.recode.varsites.phy (1.44 kB)

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missing_05_minDP2mac2minq30.recode.varsites.phy (6.58 kB)

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missing_10_minDP2mac2minq30.recode.varsites.phy (24.83 kB)

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missing_80_minDP2mac2minq30.recode.min4.phy (14.66 MB)

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Raw sequenced indexes and phylip alignments for the Seychelles caecilian phylogenomic study.

dataset

posted on 2024-11-29, 14:03 authored by Miranda SherlockMiranda Sherlock

ddRADseq data from a single 300 cycle NextSeq run using a high-output kit.Raw sequence data with barcodes required to demultiplex. Contains 38 individuals: two Hypogeophis montanus, 3 H. brevis, 5 H. sechellensis and 4 each of H. pti, H. larvatus, H. alternans, H. rostratus, Praslinia cooperi, Gegeneophis ramaswamii and Idiocranium russeli.

Phylip format alignments with variable sites only. Filtered for between 0 and 80% maximum missing data per locus, minor allele count of 2, minimum read depth 2 and minimum read quality of 30. Includes the final alignment used in the study with 50% missing data allowed 'filtered_mac2_minq30_missing50_minDP2.varsites.phy'. Contains 37 samples from the caecilian species Hypogeophis montanus, Hypogeophis pti, Hypogeophis brevis, Hypogeophis sechellensis, Hypogeophis larvatus, Hypogeophis rostratus, Hypogeophis alternans, Praslinia cooperi, Gegeneophis ramaswamii and Idiocranium russeli.