Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

Ilves KL, López-Fernández H

Date Published: January 7, 2014

DOI: http://dx.doi.org/10.5061/dryad.298qm

 

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Title Andinoacara pulcher sorted BAM file
Downloaded 15 times
Description Sorted BAM file for Andinoacara pulcher generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download AndinoacaraStandaloneFiltered_Ref923_Pair...ed.bam (445.3 Mb)
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Title Biotoecus dicentrarchus sorted BAM file
Downloaded 11 times
Description Sorted BAM file for Biotoecus dicentrarchus generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download BiotoecusStandaloneFiltered_Ref923_Paired...ed.bam (554.0 Mb)
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Title Cichla temensis sorted BAM file
Downloaded 13 times
Description Sorted BAM file for Cichla temensis generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download CichlaStandaloneFiltered_Ref923_PairedEnd...ed.bam (588.2 Mb)
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Title Crenicichla frenata sorted BAM file
Downloaded 17 times
Description Sorted BAM file for Crenicichla frenata generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download CrenicichlaStandaloneFiltered_Ref923_Pair...ed.bam (596.2 Mb)
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Title Etroplus suratensis sorted BAM file
Downloaded 11 times
Description Sorted BAM file for Etroplus suratensis generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download EtroplusStandaloneFiltered_Ref923_PairedE...ed.bam (363.9 Mb)
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Title ‘Geophagus’ brasiliensis sorted BAM file
Downloaded 20 times
Description Sorted BAM file for ‘Geophagus’ brasiliensis generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download GeophagusStandaloneFiltered_Ref923_Paired...ed.bam (486.9 Mb)
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Title Herichthys cyanoguttatus sorted BAM file
Downloaded 12 times
Description Sorted BAM file for Herichthys cyanoguttatus generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download HerichthysStandaloneFiltered_Ref923_Paire...ed.bam (425.1 Mb)
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Title Heterochromis multidens sorted BAM file
Downloaded 19 times
Description Sorted BAM file for Heterochromis multidens generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download HeterochromisStandaloneFiltered_Ref923_Pa...ed.bam (496.8 Mb)
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Title Reference sequences from Oreochromis niloticus
Downloaded 11 times
Description List of 923 reference sequences (FASTA format) from Oreochromis niloticus used for mapping and assembly.
Download Oreochromis_Refseq_923.fna (1.032 Mb)
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Title Oreochromis niloticus sorted BAM file
Downloaded 12 times
Description Sorted BAM file for Oreochromis niloticus generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download OreochromisStandaloneFiltered_PairedEndan...ed.bam (637.5 Mb)
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Title Paratilapia polleni sorted BAM file
Downloaded 46 times
Description Sorted BAM file for Paratilapia polleni generated using SAMtools. Mapping and assembly of reads was conducted with bowtie2 version 2.1.0 using the 'very sensitive' preset parameters, with a maximum fragment length for paired-end alignments (-X) of 600, with the 923 tilapia exons as the reference.
Download ParatilapiaStandaloneFiltered_Ref923_Pair...ed.bam (474.4 Mb)
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Title Alignment files for exons captured for all ten species
Downloaded 56 times
Description Alignment files for exons captured for all ten species plus the reference sequence from the Nile tilapia (Oreochromis niloticus). Each individual exon alignments was sorted into one of three categories: 'good', 'passable', or 'poor'. Only alignments in the categories 'good' and 'passable' categories were used for phylogenetic analysis. Included are the concatenated alignments used for Bayesian (MrBayes; nexus format) and maximum likelihood (RAxML; phylip format) phylogenetic analyses and individual exon alignments (phylip format) used in RAxML bootstrap analyses that were ultimately analyzed in a species tree framework using MP-EST.
Download Ilves&Lopez-Fernandez.MER_alignments.zip (9.352 Mb)
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Title Summary of steps
Downloaded 325 times
Description This file describes the steps used to identify SCP exons across 5 cichlid genomes, and process Illumina MiSeq paired-end sequence data from 923 exons across a broad phylogenetic range of 10 cichlid species. This is most certainly not an elegant or efficient way to conduct these searches & analyses [efficiency could be greatly improved through more automation (i.e., use of scripts)], but the steps below are feasible by those with minimal programming expertise (and a lot of patience).
Download Ilves&Lopez-Fernandez_SummaryOfSteps.txt (21.21 Kb)
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Title Sequence files
Downloaded 75 times
Description Consensus sequences in FASTA format for all exons captured, generated with the following quality filters: base and mapping qualities of at least 20 and a minimum depth of coverage of 10. Sequence positions that did not meet all of these criteria are coded as N. Only sequences with a minimum of 50 bases are included. Each file is named with the ENSEMBL exon ID for Oreochromis niloticus and the genus name of the taxon.
Download Sequences_min50bases.zip (5.501 Mb)
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When using this data, please cite the original publication:

Ilves KL, López-Fernández H (2014) A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Molecular Ecology Resources 14(4): 802–811. http://dx.doi.org/10.1111/1755-0998.12222

Additionally, please cite the Dryad data package:

Ilves KL, López-Fernández H (2014) Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.298qm
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