Data and code supporting the publication 'Somatic Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes'

The following data is provided: WORM_all_18S_filtered_Bunonema_outgroup.fasta : all 18S sequences used for producing the phylogeny WORM_all_28S_filtered_Bunonema_outgroup.fasta : the same for 28S sequences .nwk files: the individual 18S, 28S and 18S+28S combined trees, in Newick format Kiontke_accessions.tsv : a table, modified from supplementary table 1 of the following paper: 10.1016/j.cub.2007.10.061 The following code is provided: extract_SILVA_sequences.py : extracts sequences from SILVA, and compares them with those in the fasta sequences above. The idea is to take anything we had sequenced ourselves, and compare it to what is in public databases. We then used what was publically-available when the latter were more complete than our own sequencing. produce_18S_and_28S_phylogeny.sh : a bash script that produces filtered sequences, alignments, and phylogenetic trees. It runs the python script above This code enables reproducing the phylogenies. To run the bash script, you need to first obtain the right bioinformatic tools. For this I recommend mamba with which you can obtain the right tools with the definition file mamba_env.yaml provided here: `mamba env create -f mamba_env.yaml`. You will in addition have to install the aligner `mafft` yourself from source Contact: brice.letcher[at]ens-lyon.fr; marie.delattre[at]ens-lyon.fr