A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility – from order to species

Dataset includes: 1) Three .tre files; Astral LPP, Astral polytomy test, and IQ-tree ultra-fast bootstrap. 2) List of probes in .csv format a total of 46,893 probes designed for 446 loci and totally 5.6Mbps. This file can be used to directly order the rodent418probe set from Agilent of similar company. The first 25,116 probes are new rodent specific probes and are labeled as follows: species, Name of locus, probe number Example: mR001p1 = mouse locus 1 probe 1 The species key is as follows; m = mouse, Mus musculus, genome version mm10 k = Ord's kangaroo rat, Dipodomys ordii, genome version dipOrd1 g = guinea pig, Cavia porcellus, genome version cavPor3 s = 13-lined ground squirrel, Ictidomys tridecemlineatus , genome version speTri2 c = Chinese hamster, Crietulus griseus , genome version criGri1 gr = Gerbilus robustus (from the sequences you sent me) sm = Sigmodon mascotensis (from the sequences you sent me) n = Nesomys rufus (from the sequences you sent me) This covers 239 new rodent probes (labeled R001 - R239) as well as a set for RAG1 and IRBP (labeled as such). This file also includes the vertebrate probes (n=21,777) from the 205 loci that passed the filtering. These are the same probes from Lemmon et al. 2012 and are labeled the same names as in the paper had (frist and L then the locus number then a species abbreviation then probe number, i.e. L5D1 is locus 5 designed from Danio rerio probe 1). 3) Full sequecnes for all new rodent targets in .csv format. 4) Reference sequences pulled from the mm10 genome in .fasta format used for retrival of targets after sequencing.