The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-exon junctions from RNA-seq data. It takes Subread less than 20 minutes to map 10 million 100bp reads using one thread. Its running time remains nearly the same when mapping longer reads thanks to the high scalability of the seed-and-vote paradigm. Subread and Subjunc can be used to map reads generated from all major sequencing platforms including Illumina GA/HiSeq, Roche 454, ABI SOLiD and Ion Torrent. They can run on both Linux/unix and Mac computers. Subread and Subjunc were published in Nucleic Acids Research in 2013.