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Muntiacus muntjak and Muntiacus reevesi supporting files

Mudd, Austin, University of California, Berkeley, https://orcid.org/0000-0003-0371-8555
Bredeson, Jessen, University of California, Berkeley
Baum, Rachel, University of California, Berkeley, https://orcid.org/0000-0002-6419-5279
Hockemeyer, Dirk, University of California, Berkeley, https://orcid.org/0000-0002-5598-5092
Rokhsar, Daniel, University of California, Berkeley
amudd@berkeley.edu, jessenbredeson@berkeley.edu, rachel_baum@berkeley.edu, hockemeyer@berkeley.edu, dsrokhsar@gmail.com
Published Dec 16, 2019 on Dryad. https://doi.org/10.6078/D1KT16

Cite this dataset

Mudd, Austin et al. (2019). Muntiacus muntjak and Muntiacus reevesi supporting files [Dataset]. Dryad. https://doi.org/10.6078/D1KT16

Abstract

Available Files:

Mmuntjak.cds.fasta.gz - Nucleotide sequences of the coding regions from M. muntjak gene annotations.

Mmuntjak.gff.gz - Gene annotations for M. muntjak from Gene Model Mapper (v1.5.3).

Mmuntjak.pep.fasta.gz - Peptide sequences of the coding regions from M. muntjak gene annotations.

Mmuntjak.repeat_lib.fasta.gz - De novo repeats from RepeatModeler (v1.0.11) for M. muntjak as well as ancestral Cetartiodactyla repeats from RepBase (downloaded November 8, 2018).

Mreevesi.cds.fasta.gz - Nucleotide sequences of the coding regions from M. reevesi gene annotations.

Mreevesi.gff.gz - Gene annotations for M. reevesi from Gene Model Mapper (v1.5.3).

Mreevesi.pep.fasta.gz - Peptide sequences of the coding regions from M. reevesi gene annotations.

Mreevesi.repeat_lib.fasta.gz - De novo repeats from RepeatModeler (v1.0.11) for M. reevesi as well as ancestral Cetartiodactyla repeats from RepBase (downloaded November 8, 2018).

Muntjac.timetree.nexus - Nexus format phylogenetic tree derived from phylogenetic tree Muntjac.tree.newick. Divergence time confidence intervals from TimeTree were input into MEGA7 (v7.0.26), using the Reltime method and the GTR+Gamma model to create a time tree.

Muntjac.tree.newick - Newick format phylogenetic tree based on fourfold degenerate sites and constructed with RAxML (v8.2.11) using the GTR+Gamma model of substitution with outgroup B. taurus.

Funding

National Institute of General Medical Sciences, Award: R01GM086321

Eunice Kennedy Shriver National Institute of Child Health and Human Development, Award: R01HD080708

National Cancer Institute, Award: R01CA196884