Fern Tree of Life (FTOL) input data

<p>The data included here are used in a pipeline that (mostly) automatically generates a maximally sampled fern phylogenetic tree based on plastid sequences in GenBank (github.com/fernphy/ftol).<br> <br> The first step is to download the latest release of GenBank data from the NCBI GenBank FTP site (ftp.ncbi.nlm.nih.gov/genbank/) and use it to create a local database of fern sequences. This is done with custom R scripts contained in github.com/fernphy/ftol, in particular setup_gb.R (github.com/fernphy/ftol/blob/main/R/setup_gb.R).<br> <br> Next, a set of reference FASTA files for 79 target loci (one per locus; ref_aln.tar.gz) is generated.

These include 77 protein-coding genes based on a list of 83 genes (Wei et al. 2017) that was filtered to only genes that show no evidence of duplication, plus two spacer regions (trnL-trnF and rps4-trnS). Each FASTA file in ref_aln.tar.gz includes one representative (longest) sequence per avaialable fern genus. This is done with prep_ref_seqs_plan.R (github.com/fernphy/ftol/blob/main/prep_ref_seqs_plan.R).<br> <br> Sequences matching the target loci are then extracted from each accession in the local database using the FASTA files contained in ref_aln.tar.gz as references with the “Reference_Blast_Extract.py” script of superCRUNCH (Portik and Wiens 2020).<br> <br> The extracted sequences are aligned with MAFFT (Katoh et al. 2002), phylogenetic analysis is done using IQ-TREE (Nguyen et al. 2015) and divergence times estimated with treePL (Smith and O’Meara 2012).<br> <br> For additional methodological details, see:<br> <br> Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. 2022.