MANIFEST.in
README
RELEASE
VERSION
install.sh
setup.py
bin/rsq
examples/00simple/00Examples.sh
examples/00simple/sce_S1_demo.tab
examples/00simple/sce_V1_demo.tab
examples/00simple/sce_genes_demo.fasta
examples/01isoform/.fc
examples/01isoform/.fs
examples/01isoform/01Examples.sh
examples/01isoform/hg19_demo.gpd
examples/01isoform/hg19_demo_S.wig
examples/01isoform/hg19_demo_V.wig
examples/02advanced/02Examples.sh
examples/02advanced/demo01.fc
examples/02advanced/demo01.fd
examples/02advanced/demo01.fs
examples/02advanced/demo02.fc
examples/02advanced/demo02.fd
examples/02advanced/demo02.fs
examples/02advanced/known.fs
external/RNAlib/makefile
external/RNAlib/fold/COPYING
external/RNAlib/fold/LPfold.c
external/RNAlib/fold/LPfold.h
external/RNAlib/fold/Lfold.c
external/RNAlib/fold/Lfold.h
external/RNAlib/fold/MEA.c
external/RNAlib/fold/MEA.h
external/RNAlib/fold/PS_dot.c
external/RNAlib/fold/PS_dot.h
external/RNAlib/fold/ProfileAln.c
external/RNAlib/fold/ProfileAln.h
external/RNAlib/fold/ProfileDist.c
external/RNAlib/fold/RNAstruct.c
external/RNAlib/fold/RNAstruct.h
external/RNAlib/fold/alicircfold.inc
external/RNAlib/fold/alifold.c
external/RNAlib/fold/alifold.h
external/RNAlib/fold/alipfold.c
external/RNAlib/fold/aln_util.c
external/RNAlib/fold/aln_util.h
external/RNAlib/fold/circfold.inc
external/RNAlib/fold/cofold.c
external/RNAlib/fold/cofold.h
external/RNAlib/fold/common.h
external/RNAlib/fold/config.h
external/RNAlib/fold/dist_vars.c
external/RNAlib/fold/dist_vars.h
external/RNAlib/fold/duplex.c
external/RNAlib/fold/duplex.h
external/RNAlib/fold/edit_cost.h
external/RNAlib/fold/energy_const.h
external/RNAlib/fold/energy_par.c
external/RNAlib/fold/energy_par.h
external/RNAlib/fold/findpath.c
external/RNAlib/fold/findpath.h
external/RNAlib/fold/fold.c
external/RNAlib/fold/fold.h
external/RNAlib/fold/fold_vars.c
external/RNAlib/fold/fold_vars.h
external/RNAlib/fold/intloops.h
external/RNAlib/fold/inverse.c
external/RNAlib/fold/inverse.h
external/RNAlib/fold/list.c
external/RNAlib/fold/list.h
external/RNAlib/fold/makefile
external/RNAlib/fold/naview.c
external/RNAlib/fold/pair_mat.h
external/RNAlib/fold/params.c
external/RNAlib/fold/params.h
external/RNAlib/fold/part_func.c
external/RNAlib/fold/part_func.h
external/RNAlib/fold/part_func_co.c
external/RNAlib/fold/part_func_co.h
external/RNAlib/fold/part_func_up.c
external/RNAlib/fold/part_func_up.h
external/RNAlib/fold/profiledist.h
external/RNAlib/fold/read_epars.c
external/RNAlib/fold/ribo.c
external/RNAlib/fold/ribo.h
external/RNAlib/fold/stringdist.c
external/RNAlib/fold/stringdist.h
external/RNAlib/fold/subopt.c
external/RNAlib/fold/subopt.h
external/RNAlib/fold/treedist.c
external/RNAlib/fold/treedist.h
external/RNAlib/fold/utils.c
external/RNAlib/fold/utils.h
external/RNAlib/plot/DrawingConstants.h
external/RNAlib/plot/ErrorChecker.h
external/RNAlib/plot/MaxExpect.cpp
external/RNAlib/plot/MaxExpect.h
external/RNAlib/plot/MaxExpectStack.cpp
external/RNAlib/plot/MaxExpectStack.h
external/RNAlib/plot/ParseCommandLine.cpp
external/RNAlib/plot/ParseCommandLine.h
external/RNAlib/plot/RNA.cpp
external/RNAlib/plot/RNA.h
external/RNAlib/plot/ReadMe.txt
external/RNAlib/plot/StructureImageHandler.cpp
external/RNAlib/plot/StructureImageHandler.h
external/RNAlib/plot/TProgressDialog.cpp
external/RNAlib/plot/TProgressDialog.h
external/RNAlib/plot/algorithm.cpp
external/RNAlib/plot/algorithm.h
external/RNAlib/plot/alltrace.cpp
external/RNAlib/plot/alltrace.h
external/RNAlib/plot/arrayclass.cpp
external/RNAlib/plot/arrayclass.h
external/RNAlib/plot/boltzmann.h
external/RNAlib/plot/defines.h
external/RNAlib/plot/dotarray.cpp
external/RNAlib/plot/dotarray.h
external/RNAlib/plot/draw.cpp
external/RNAlib/plot/draw.h
external/RNAlib/plot/extended_double.cpp
external/RNAlib/plot/extended_double.h
external/RNAlib/plot/forceclass.cpp
external/RNAlib/plot/forceclass.h
external/RNAlib/plot/gamma.h
external/RNAlib/plot/makefile
external/RNAlib/plot/makefile2
external/RNAlib/plot/outputconstraints.cpp
external/RNAlib/plot/outputconstraints.h
external/RNAlib/plot/pfunction.cpp
external/RNAlib/plot/pfunction.h
external/RNAlib/plot/platform.h
external/RNAlib/plot/probknot.cpp
external/RNAlib/plot/probknot.h
external/RNAlib/plot/random.cpp
external/RNAlib/plot/random.h
external/RNAlib/plot/rna_library.cpp
external/RNAlib/plot/rna_library.h
external/RNAlib/plot/stackclass.cpp
external/RNAlib/plot/stackclass.h
external/RNAlib/plot/stackstruct.cpp
external/RNAlib/plot/stackstruct.h
external/RNAlib/plot/stochastic.cpp
external/RNAlib/plot/stochastic.h
external/RNAlib/plot/structure.cpp
external/RNAlib/plot/structure.h
external/RNAlib/plot/substructure.cpp
external/RNAlib/plot/thermodynamics.cpp
external/RNAlib/plot/thermodynamics.h
external/RNAlib/wRNA/a.out
external/RNAlib/wRNA/makefile
external/RNAlib/wRNA/test.cpp
external/RNAlib/wRNA/wRNA.cpp
external/RNAlib/wRNA/wRNA.h
rsq.egg-info/PKG-INFO
rsq.egg-info/SOURCES.txt
rsq.egg-info/dependency_links.txt
rsq.egg-info/requires.txt
rsq.egg-info/top_level.txt
src/__init__.py