TopHat Authors

Contact:
  tophat.cufflinks@gmail.com
  
Cole Trapnell wrote the original TopHat program. TopHat is built on Bowtie,
  which was written by Ben Langmead and Cole Trapnell.
Daehwan Kim and Geo Pertea added support for SOLiD reads, Bowtie 2 and many 
  other features and improvements leading to the release of TopHat2, of which
  they are the current maintainers.

SAMtools version 0.1.18 is used in TopHat2 and its sources are included in 
  TopHat2's source release starting with version 2.0.13; SAMtools 0.1.18 was
  written primarily by Heng Li and Bob Handsaker.
   
The SeqAn-1.3 library is used in TopHat and some of its sources are included 
  in TopHat source releases; its authors are Andreas Doring, David Weese, 
  Tobias Rausch, and Knut Reinert.

The IntervalTree library is used by TopHat in its fusion-calling pipeline; 
  its authors are Chaim-Leib Halbert and Konstantin Tretyakov. This package
  is released under the Apache 2.0 license.

The SortedContainers library is used by TopHat in its fusion-calling
  pipeline; its author is Grant Jenks. This package is released under the
  Apache 2.0 license.

Websites:
 TopHat:                http://ccb.jhu.edu/software/tophat
 Bowtie:                http://bowtie-bio.sourceforge.net/bowtie2
 Samtools:              http://samtools.sourceforge.net
 SeqAn:                 http://www.seqan.de
 IntervalTree:          https://github.com/chaimleib/intervaltree
 SortedContainers:      http://www.grantjenks.com/docs/sortedcontainers/