Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

McGee MD, Faircloth BC, Borstein SR, Zheng J, Hulsey CD, Wainwright PC, Alfaro ME

Date Published: January 27, 2016

DOI: http://dx.doi.org/10.5061/dryad.9pg8d

 

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Title SRA-files.xlsx
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Description Accession numbers for raw-reads in NCBI SRA.
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Title trinity-assemblies-for-dryad.tar.gz
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Description De novo Trinity (trinityrnaseq_r2013-02-25) assemblies of raw-reads for all individuals included in study.
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Title outgroup-data.tar.gz
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Description Outgroup data included in analysis from genome-enabled cichlids.
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Title 11-20-2014-malfaro-cichlids-taxa.conf
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Description Configuration file used with PHYLUCE for taxon-set extraction.
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Title skull-mobility-contig-and-alignment-data.tar.gz
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Description UCE contigs, alignments, trimmed alignments, coverage information, and configuration and log files used in all phylogenetic analyses.
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Title mafft-gblocks-clean-95p-complete-raxml.tar.gz
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Description Partition-finder and RAxML input/output files for ML analysis of the 95 % complete data set.
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Title mafft-gblocks-clean-95p-complete-EXABAYES.tar.gz
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Description ExaBayes output files for Bayesian analysis of the 95 % complete data set.
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Title mafft-gblocks-clean-75p-complete-raxml.tar.gz
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Description Partition-finder and RAxML input/output files for ML analysis of the 75 % complete data set.
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Title mafft-gblocks-clean-75p-complete-EXABAYES.tar.gz
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Description ExaBayes output files for Bayesian analysis of the 75 % complete data set.
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Title phylogenetic-analysis-steps.txt
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Description Steps used during the phylogenetic analysis. All used the PHYLUCE software package (available from: https://github.com/faircloth-lab/phyluce).
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Title fish-uce-1k-probes.fasta.gz
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Description Fasta file detailing probes targeting UCEs in Acanthomorphs.
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Title all-tre-files.tar.gz
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Description An archive of all trees generated for the manuscript text in Newick format.
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When using this data, please cite the original publication:

McGee MD, Faircloth BC, Borstein SR, Zheng J, Hulsey CD, Wainwright PC, Alfaro ME (2016) Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Proceedings of the Royal Society B 283(1822): 20151413. http://dx.doi.org/10.1098/rspb.2015.1413

Additionally, please cite the Dryad data package:

McGee MD, Faircloth BC, Borstein SR, Zheng J, Hulsey CD, Wainwright PC, Alfaro ME (2016) Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.9pg8d
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