data_old.Rmd

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Here you can find data I've generated in the previous years, including genomes, genome annotations, repeats and tools used.


####Drosophila innubila
Data generated for [Hill, Koseva and Unckless (2019) The genome of *Drosophila innubila* reveals lineage-specific patterns of selection in immune
genes.](files/TH_MBE_2019.pdf)

* [Genome sequence in fasta format.](data/Dinnubila.fa.tar.gz)
* [Genome gene annotation.](data/Dinnubila.gff.tar.gz)
* [Genome repeat sequences in fasta format.](data/Dinnubila.repeats.fa.tar.gz)
* [Transcriptome generated from RNAseq information]()
* [Genome repeat annotation.](data/Dinnubila.fa.out.gff.tar.gz)
* [dN/dS per gene on each branch of the quinaria group](data/Dinnubila.dNdS.txt.tar.gz)


####Drosophila innubila Nudivirus
Data generated for [Hill and Unckless (2018) The dynamic evolution of Drosophila innubila Nudivirus.](files/TH_IGE_2018.pdf)

* [Genome sequence in fasta format.](data/DiNV_CH01M.fa.tar.gz)
* [Genome gene annotation.](data/DiNV_CH01M.gff.tar.gz)

####Balancing selection in antimicrobial peptides
Data generated for [Chapman, Hill and Unckless (2019) Balancing selection drives maintenance of genetic variation in *Drosophila* antimicrobial peptides.](files/TH_GBE_2019.pdf)

* [List of immune genes with functional annotation.](https://www.epfl.ch/labs/lemaitrelab/wp-content/uploads/2018/12/drosophila-genes-potentially.xls)
* [DPGP data dump.](http://johnpool.net/genomes.html)
* [Database of DPGP strains.](http://johnpool.net/TableS1_individuals.xls)

####dudeML
Data generated for [Hill & Unckless (2019) A deep-learning approach for detecting copy number variants in next-generation sequencing data.](files/TH_dudeML_2019.pdf)

* [dudeML page containing manual and download information.](https://github.com/tomh1lll/dudeml)