mosstrap-masked-coding.tar

RNA-Seq was conducted on Illumina Hi-Seq 2000 platform, and reads were quality trimmed using Trimmomatic. De novo transcriptome assemblies were generated using Trinity, which can produce many isoforms. We used a phylogenetic approach to decide whether to retain isoforms. Transcripts which contained a valid protein with a BLASTp hit to a known land plant proteome were clustered using mcl, and gene trees were built from sequences in each cluster. To generate the "masked" dataset, the gene trees were searched for monophyletic clades containing sequences from the same species. Only one transcript per clade was retained, and the others were pruned from further analysis. This archive contains a multi-FASTA file of coding (DNA) sequences for each of the transcriptomes generated for the study.