Comparative genomics of ten new Caenorhabditis species

Phylogenomic analysis

ASTRAL_species_tree.ASTRAL_branch_lengths.nwk: Species tree generated by ASTRAL-III with branch lengths in coalescent units

ASTRAL_species_tree.RAxML_branch_lengths.nwk: Species tree generated by ASTRAL-III with branch lengths in substitutions per site as estimated by RAxML (GTR+Γ)

Caenorhabditis_33species_1988loci_supermatrix.fas: Supermatrix composed of 1988 single-copy loci 27 of 33 species analysed

Orthogroups.txt: Original orthology clustering file

PhyloBayes_species_tree.nwk: Species tree generated by PhyloBayes MPI (CAT-GTR+Γ)

RAxML_species_tree.nwk: Species tree generated by RAxML (GTR+Γ)

singlecopy_orthologues_redundantseqs_removed.txt: Orthogroups used in analysis, after removing redundant sequences

Intron analysis

Orthogroups_990_0missing_5hetero_paraloguesremoved_withCDSalignments.txt: Single copy orthogroups.txt file (note: this is after removing redundant sequences arising from uncollapsed heterozygosity and removing orthogroups containing paralogues)

genome_gene_structure_stats.tsv: File containing gene structure and genome size statistics

Notch-like receptor analysis

OG0000658.below700removed.fa: FASTA file of all sequences in orthogroup that were 700 amino acids or longer.

OG0000658.below700removed.fa.aln: alignment of the above FASTA file

OG0000658.below700removed.fa_ProSiteProfiles.tsv: InterProScan search results of the above FASTA file using the ProSiteProfiles database (release 2017_09)

OG0000658.txt: Line from orthology clustering with all (including those below 700 amino acid) sequence IDs

RAxML_bipartitions.OG0000658.below700removed.nwk: RAxML ML tree of the above alignment file with bootstrap support values

extract_branch_lengths.py: Python script used to extract branch lengths