This paper studies sequencing and mapping methods that rely solely on pooling and shotgun sequencing of clones. First, we scrutinize and improve the recently proposed Clone-Array Pooled Shotgun Sequencing (CAPSS) method, which delivers a BAC-linked assembly of a whole genome sequence. Secondly, we introduce a novel physical mapping method, called Clone-Array Pooled Shotgun Mapping (CAPS-MAP), which computes the physical ordering of BACs in a random library. Both CAPSS and CAPS-MAP construct subclone libraries from pooled genomic BAC clones.