/usr/bin/bam2fastx
/usr/bin/bam_merge
/usr/bin/bed_to_juncs
/usr/bin/contig_to_chr_coords
/usr/bin/fix_map_ordering
/usr/bin/gtf_juncs
/usr/bin/gtf_to_fasta
/usr/bin/juncs_db
/usr/bin/long_spanning_reads
/usr/bin/map2gtf
/usr/bin/prep_reads
/usr/bin/sam_juncs
/usr/bin/samtools_0.1.18
/usr/bin/segment_juncs
/usr/bin/sra_to_solid
/usr/bin/tophat2
/usr/bin/tophat
/usr/bin/tophat-fusion-post
/usr/bin/tophat_reports
You may install this package on Debian with
apt-get
install tophat