Data from: Episodic radiations in the fly tree of life

 

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Title FLYTREEmitoGeneAln
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Description Nucleotide alignments in FASTA format for mitochondrial genes sequenced in the FLYTREE PROJECT. These sequences were used in Wiegmann et al. 2011 PNAS 108:5690 (doi:10.1073/pnas.1012675108) and in Caravas and Friedrich 2012 Syst. Ent. (doi: 10.1111/j.1365-3113.2012.00657.x)
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Title FLYTREENuclearGenes_ALN
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Description Nucleotide alignments in FASTA format for all nuclear genes sequenced in the FLYTREE PROJECT. These sequences were used in Wiegmann et al. 2011 PNAS 108:5690 (doi:10.1073/pnas.1012675108) and in Caravas and Friedrich 2012 Syst. Ent. (doi: 10.1111/j.1365-3113.2012.00657.x)
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Title 18SrDNA_alnFLYTREE
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Description Alignment of dipteran 18S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title 28SrDNA_alnFLYTREE
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Description Alignment of dipteran 28S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title AATS_Exon1alnFLYTREE
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Description Alignment of dipteran AATS1 gene sequences from the FLYTREE project in fasta format.
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Title CAD_noIntrons.alnFLYTREE
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Description Alignment of dipteran CAD (= CPSase, rudimentary) gene sequences from the FLYTREE project in fasta format.
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Title G6PD_alnFLYTREE
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Description Alignment of dipteran G6PD gene sequences from the FLYTREE project in fasta format.
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Title GART_alnFLYTREE
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Description Alignment of dipteran GART gene sequences from the FLYTREE project in fasta format.
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Title PEPCK_alnFLYTREE
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Description Alignment of dipteran PEPCK gene sequences from the FLYTREE project in fasta format.
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Title PER_NoIntrons_alnFLYTREE
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Description Alignment of dipteran period (per) gene sequences from the FLYTREE project in fasta format.
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Title PGDintrons_alnFLYTREE
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Description Alignment of dipteran PGD gene sequences, with introns included in the alignment,from the FLYTREE project in fasta format.
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Title PGDnointrons_alnFLYTREE
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Description Alignment of dipteran PGD gene sequences from the FLYTREE project in fasta format.
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Title PUG_C1THFsynthase_alnFLYTREE
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Description Alignment of dipteran CH1-THF synthase (pug) gene sequences from the FLYTREE project in fasta format.
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Title SINA_alnFLYTREE
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Description Alignment of dipteran SINA gene sequences from the FLYTREE project in fasta format.
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Title SNF_alnFLYTREE
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Description Alignment of dipteran sans fille (snf) gene sequences from the FLYTREE project in fasta format.
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Title SYX1A_alnFLYTREE
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Description Alignment of dipteran SYX1A gene sequences from the FLYTREE project in fasta format.
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Title TPI_noIntrons_alnFLYTREE
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Description Alignment of dipteran TPI gene sequences from the FLYTREE project in fasta format.
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Title mtAtp6-alnFLYTREE
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Description Alignment of dipteran mitochondrial ATP6 gene sequences from the FLYTREE project in fasta format.
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Title mtAtp8-alnFLYTREE
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Description Alignment of dipteran mitochondrial ATP8 gene sequences from the FLYTREE project in fasta format.
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Title Cox1-alnFLYTREE
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Description Alignment of dipteran mitochondrial CO1 gene sequences from the FLYTREE project in fasta format.
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Title Cox2-alnFLYTREE
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Description Alignment of dipteran mitochondrial COII (cox2) gene sequences from the FLYTREE project in fasta format.
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Title Cox3-alnFLYTREE
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Description Alignment of dipteran mitochondrial CO-III (Cox3) gene sequences from the FLYTREE project in fasta format.
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Title Cytb-alnFLYTREE
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Description Alignment of dipteran mitochondrial cyt-b gene sequences from the FLYTREE project in fasta format.
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Title Large_rRNA16S-alnFLYTREE
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Description Alignment of dipteran mitochondrial 16S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Small_rRNA12S-alnFLYTREE
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Description Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Nad1-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH1 gene sequences from the FLYTREE project in fasta format.
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Title Nad2-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH2 gene sequences from the FLYTREE project in fasta format.
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Title Nad3-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH3 gene sequences from the FLYTREE project in fasta format.
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Title Nad4-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH4 gene sequences from the FLYTREE project in fasta format.
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Title Nad4L-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH4L gene sequences from the FLYTREE project in fasta format.
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Title Nad5-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH5 gene sequences from the FLYTREE project in fasta format.
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Title Nad6-alnFLYTREE
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Description Alignment of dipteran mitochondrial NADH6 gene sequences from the FLYTREE project in fasta format.
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Title Small_rRNA12S-alnFLYTREE
Downloaded 36 times
Description Alignment of dipteran mitochondrial 12S ribosomal RNA gene sequences from the FLYTREE project in fasta format.
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Title Textnames
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Description This file resolves the identity of taxon name codes used in the phylogenetic data sets below. You can also find information about all of these name codes at : http://www.inhs.uiuc.edu/research/flytreephp/flytree/index.php
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Title FLY dataset annotations
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Description this is an EXCEL file that gives annotations by position numbers for the combined datasets (see below). Note.. the mitochondrial genes are just annotated as 'mito'.
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Title 28S.aln5.22.09
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Description This is the uncut 28S rDNA file for T2+T1, with annotations about included regions. Ribosomal genes are complex to align across deep divergences (240 million years for flies). That means that divergent domains (expansion regions are excluded in most phylogenetic analyses of this gene.), so the annotations in this file (at the bottom) correspond to positions that are cut-out (excluded) in our phylogenetic analysis. If you sequenced 28S this will allow you to fit your sequence into our alignment without confusion about missing pieces. Brachyceran or only Schizophoran sequences were separated from lower Diptera for some regions in this alignment, in order to include alignable regions within these sections for just higher flies. The cut version of this file is FLY2.28s.nex (not annotated).
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Title fly2.28s
Downloaded 40 times
Description 28S rDNA alignment for phylogenetic analysis with ambiguous alignment regions The cut version of 28s.aln.5.22.09.nex
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When using this data, please cite the original publication:

Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim J-W, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeates DK (2011) Episodic radiations in the fly tree of life. Proceedings of the National Academy of Sciences of the United States of America 108(14): 5690-5695. http://dx.doi.org/10.1073/pnas.1012675108

Additionally, please cite the Dryad data package:

Wiegmann BM, Trautwein MD, Winkler IS, Barr NB, Kim J, Lambkin C, Bertone MA, Cassel BK, Bayless KM, Heimberg AM, Wheeler BM, Peterson KJ, Pape T, Sinclair BJ, Skevington JH, Blagoderov V, Caravas J, Kutty SN, Schmidt-Ott U, Kampmeier GE, Thompson FC, Grimaldi DA, Beckenbach AT, Courtney GW, Friedrich M, Meier R, Yeates DK (2011) Data from: Episodic radiations in the fly tree of life. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.21nf3
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