Bedrock radioactivity influences the rate and spectrum of mutation - Orthologous genes

Alignments of the 2490 orthologous genes used in the article "Natural Bedrock radioactivity influences the rate and spectrum of mutation" to estimate the mutational spectrum and synonymous substitution rate. To compute accurate synonymous substitution rate, we removed genes with short sequences (<half of the alignment) and genes strongly supporting another phylogeny using ProfileNJ (Noutahi et al. 2016) with a bootstrap threshold of 90%, resulting in a subset of 769 genes listed in the file "List_769_1-to-1_orthologs_EvolutionRate.txt". Transcriptome paired-end reads used to define these orthologous genes have been deposited to the European Nucleotide Archive and are available under the study ID PRJEB14193. Sequences were aligned with Prank (Löytynoja & Goldman 2008) using a codon model and sites ambiguously aligned were removed with Gblocks (Castresana 2000).