Comparative Genomics Of Ten New Caenorhabditis Species

<strong>Phylogenomic analysis</strong> <code>ASTRAL_species_tree.ASTRAL_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in coalescent units <code>ASTRAL_species_tree.RAxML_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in substitutions per site as estimated by RAxML (GTR+Γ) <code>Caenorhabditis_33species_1988loci_supermatrix.fas</code>: Supermatrix composed of 1988 single-copy loci 27 of 33 species analysed <code>Orthogroups.txt</code>: Original orthology clustering file <code>PhyloBayes_species_tree.nwk</code>: Species tree generated by PhyloBayes MPI (CAT-GTR+Γ) <code>RAxML_species_tree.nwk</code>: Species tree generated by RAxML (GTR+Γ) <code>singlecopy_orthologues_redundantseqs_removed.txt</code>: Orthogroups used in analysis, after removing redundant sequences <strong>Intron analysis</strong> <code>Orthogroups_990_0missing_5hetero_paraloguesremoved_withCDSalignments.txt</code>: Single copy orthogroups.txt file (note: this is after removing redundant sequences arising from uncollapsed heterozygosity and removing orthogroups containing paralogues) <code>genome_gene_structure_stats.tsv</code>: File containing gene structure and genome size statistics <strong>Notch-like receptor analysis</strong> <code>OG0000658.below700removed.fa</code>: FASTA file of all sequences in orthogroup that were 700 amino acids or longer. <code>OG0000658.below700removed.fa.aln</code>: alignment of the above FASTA file <code>OG0000658.below700removed.fa_ProSiteProfiles.tsv</code>: InterProScan search results of the above FASTA file using the ProSiteProfiles database (release 2017_09) <code>OG0000658.txt</code>: Line from orthology clustering with all (including those below 700 amino acid) sequence IDs <code>RAxML_bipartitions.OG0000658.below700removed.nwk</code>: RAxML ML tree of the above alignment file with bootstrap support values <code>extract_branch_lengths.py</code>: Python script used to extract branch lengths