Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera

Bazinet AL, Mitter KT, Davis DR, van Nieukerken EJ, Cummings MP, Mitter C

Date Published: November 25, 2016

DOI: http://dx.doi.org/10.5061/dryad.hj278

 

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Title LEP62 amino acid custom substitution rate matrix for Lepidoptera
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Description LEP62 custom amino acid substitution matrix constructed from the 5,152-gene moth+min-one-butterfly database
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Title List of 2,212 genes (orthologous groups) included in the final data matrix
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Description List of the 2,212 genes in the final data matrix, which have survived the PTP paralogy filter and are represented in at least 21 taxa. The gene numbers in this list were assigned arbitrarily during construction of our 5,152-gene moth+min-one-butterfly database. Each of these numbers, however, also corresponds to a Bombyx gene number taken from Ensembl (and hence SilkDB), as shown in the file 'bombyx_annotation_5152_OGs.txt'.
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Title lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_degen1
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Description Data matrix in fasta format for degen1 analysis
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Title lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_degen1
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Description Data matrix in Phylip format for degen1 analysis.
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Title lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_nt123
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Description Data matrix in fasta format for all-nucleotides (nt123) analyis.
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Title lep_non_ditrysia_28_taxa_2212_OGs_consensus_cols_removed_nt123
Downloaded 9 times
Description Data matrix in Phylip format for all-nucleotides (nt123) analysis.
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Title raxml_partition_by_codon_position
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Description Raxml code for partitioning by codon position.
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Title lep_ensembl_bombyx_plus_min_one_butterfly_lowsimremoved_plus_plutella_manduca_HaMStR_database
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Description The 5,152-gene moth+min-one-butterfly database, together with gene identifiers, available annotations, and profile hidden Markov models for use in ortholog search
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Title post_PTP_consensus_cds_alignments_28_taxa_2212
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Description The individual alignments for each of the 2,212 genes which survived the PTP paralog screen and are represented in at least 21 taxa.
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Title bombyx_annotation_5152_OGs.txt
Downloaded 4 times
Description Shows the correspondence between our gene numbers (left column), arbitrarily assigned during construction of our moth+min-one-butterfly database, and the Bombyx gene numbers in Ensemble/SilkD. Gene ontologies from SilkDB are included when they are available. This file is duplicated in the folder 'lep_ensembl_bombyx_plus_min_one_butterfly_lowsimremoved_plus_plutella_manduca_HaMStR_database'.
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Title Trinity_assemblies_unfiltered
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Description Complete raw Trinity assemblies
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Title ABySS_assemblies_unfiltered
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Description Complete raw ABySS assemblies (a subset of taxa only)
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When using this data, please cite the original publication:

Bazinet AL, Mitter KT, Davis DR, van Nieukerken EJ, Cummings MP, Mitter C (2017) Phylotranscriptomics resolves ancient divergences in the Lepidoptera. Systematic Entomology 42(2): 305–316. http://dx.doi.org/10.1111/syen.12217

Additionally, please cite the Dryad data package:

Bazinet AL, Mitter KT, Davis DR, van Nieukerken EJ, Cummings MP, Mitter C (2016) Data from: Phylotranscriptomics resolves ancient divergences in the Lepidoptera. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hj278
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