Next-generation phylogenomics using a Target Restricted Assembly Method

► We develop a Target Restricted Assembly Method for obtaining phylogenomic data from next-generation sequencing reads. ► This method uses BLAST searches of reads from a single Illumina lane to identify matching reads for target genes. ► Matching reads are assembled locally to produce complete single copy nuclear protein coding sequences. ► In an example with 20 species of lice (Psocodea) we recover sequences for 10 genes and perform a phylogenetic analysis.