Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

Costa IR, Prosdocimi F, Jennings WB

Date Published: July 14, 2016

DOI: http://dx.doi.org/10.5061/dryad.jn8nt

 

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Title AE171_data_files
Downloaded 6 times
Description This folder contains AE171 data saved into different file formats: AE171_concatenated.phylip contains all 171 AE loci concatenated into a supermatrix for species tree analyses. AE171_fasta singles folder contains 171 AE loci as individual fasta-formatted files. AE171_multi.nexus file contains 171 AE loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AE171_multi.phylip file contains 171 AE loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL171_nexus_singles folder contains 171 AE loci as individual nexus-formatted files.
Download AE171_data_files.zip (1.032 Mb)
Download README.txt (4.5 Kb)
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Title AE242_data_files
Downloaded 2 times
Description This folder contains AE242 data saved into different file formats: AE242_concatenated.phylip contains all 242 AE loci concatenated into a supermatrix for species tree analyses. AE242_fasta singles folder contains 242 AE loci as individual fasta-formatted files. AE242_multi.nexus file contains 242 AE loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AE242_multi.phylip file contains 242 AE loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL242_nexus_singles folder contains 242 AE loci as individual nexus-formatted files.
Download AE242_data_files.zip (1.485 Mb)
Download README.txt (4.5 Kb)
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Title AL292_data_files
Downloaded 2 times
Description This folder contains AL292 data saved into different file formats: AL292_concatenated.phylip contains all 292 loci concatenated into a supermatrix for species tree analyses. AL292_fasta singles folder contains 292 single-copy, presumably neutral, and independent anonymous loci as individual fasta-formatted files. AL292_multi.nexus file contains 292 single-copy, presumably neutral, and independent anonymous loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AL292_multi.phylip file contains 292 single-copy, presumably neutral, and independent anonymous loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL292_nexus_singles folder contains 292 single-copy, presumably neutral, and independent anonymous loci as individual nexus-formatted files.
Download AL292_data_files.zip (1.893 Mb)
Download README.txt (4.5 Kb)
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Title HKY208_data_files
Downloaded 2 times
Description This folder contains HKY208 data saved into different file formats: HKY208_multi.phylip contains all 208 AL loci found in the AL292 dataset, which fit the HKY model of substitution. These HKY-only data were analyzed separately to evaluate the effects of model selection on our results. HKY208_nexus_singles folder contains 208 single-copy, presumably neutral, and independent anonymous loci that fit the HKY model as individual nexus-formatted files.
Download HKY208_data_files.zip (592.6 Kb)
Download README.txt (4.5 Kb)
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When using this data, please cite the original publication:

Costa IR, Prosdocimi F, Jennings WB (2016) In silico phylogenomics using complete genomes: a case study on the evolution of hominoids. Genome Research 26(11): 1257-1267. http://dx.doi.org/10.1101/gr.203950.115

Additionally, please cite the Dryad data package:

Costa IR, Prosdocimi F, Jennings WB (2016) Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jn8nt
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