Reference target files for Species delimitation and diversification of the Doum palms (Hyphaene; Arecaceae) in Africa

The file PhyloPalms_loci_renamed.fasta was obtained by combining the palm reference sequences used to develop the baits to capture 176 loci as described in Heyduk et al 2016 with the Elaeis guineensis reference sequences used to develop the baits to capture 793 other loci selected to be part of the PhyloPalms kit described in Loiseau et al., 2019. It is build to be used with the program Hybpiper (Johnson et al. 2016). The PhyloPalms_Exons300_and_Heyduk.fasta file was obtained by removing exons <300 bp from the PhyloPalm references included in the PhyloPalms_loci_renamed.fasta file. These files were communicated by Sidonie Bellot. The New_ref.fasta was generated after the first run of Hybpiper (using the file PhyloPalms_loci_renamed.fasta) by selecting the longest exonic contig retrieved for each locus for the Hyphaene species and for the outgroup and was used as a reference in a second run of Hybpiper.