stochhmm

StochHMM: A free, easy to use, flexible Hidden Markov C++ library and application StochHMM is a free, easy to use, open source C++ Library and application that implements HMM from simple text files. It implements traditional HMM algorithms in addition it providing additional flexibility. The additional flexibility is achieved by allowing researchers to integrate additional data sources and application into the HMM framework. StochHMM implements standard HMM, (Preliminary) HMM with duration. It grants researchers the power to integrate additional datasets in their HMM to improve predictions. Finally, it adapts HMM algorithms to provide stochastic decoding giving researchers the ability to explore and rank sub-optimal predictions. We are providing StochHMM as a standalone application and C++ library to give researchers the ability to rapidly develop HMMs. Integrating Data Here are a few of the ways that StochHMM allows the

pax_global_header
.gitattributes
.gitignore
AUTHORS
COPYING
ChangeLog
INSTALL
LICENSE
Makefile.am
Makefile.in
NEWS
README
README.md
aclocal.m4
autom4te.cache
output.0
output.1
output.2
requests
traces.0
traces.1
traces.2
autoscan.log
config.h
config.h.in
config.status
configure
configure.ac
depcomp
examples
3_16Eddy.fa
3_16Eddy.hmm
3_17Eddy.fa
Dice.fa
Dice.hmm
Dice_explicit.hmm
Dice_short.fa
GC_SKEW.hmm
install-sh
missing
src
CDF.cpp
CDF.h
Counter.cpp
Counter.h
Doxyfile
Makefile.am
Makefile.in
MotifScorer.cpp
MotifScorer.h
PDF.cpp
PDF.h
StochHMM.cpp
StochHMM_usage.h
StochHMMlib.h
alignment.cpp
alignment.h
backward.cpp
baum_welch.cpp
bitwise_ops.cpp
bitwise_ops.h
deprecated
distributions.cpp
distributions.h
dynamic_bitset.cpp
dynamic_bitset.h
emm.cpp
emm.h
externDefinitions.cpp
externDefinitions.h
externalFuncs.cpp
externalFuncs.h
forward.cpp
forward_viterbi.cpp
hmm.cpp
hmm.h
index.cpp
index.h
lexicalTable.cpp
lexicalTable.h
modelTemplate.cpp
modelTemplate.h
nth_best.cpp
options.cpp
options.h
output.cpp
output.h
posterior.cpp
pwm.cpp
pwm.h
seqJobs.cpp
seqTracks.cpp
seqTracks.h
sequence.cpp
sequence.h
sequenceStream.cpp
sequenceStream.h
sequences.cpp
sequences.h
simpleTable.h
sparseArray.h
state.cpp
state.h
stateInfo.h
statistics.cpp
statistics.h
stochMath.cpp
stochMath.h
stochTable.cpp
stochTable.h
stochTypes.h
stoch_forward.cpp
stoch_viterbi.cpp
text.cpp
text.h
traceback_path.cpp
traceback_path.h
track.cpp
track.h
trainingSeq.cpp
trainingSeq.h
transitions.cpp
transitions.h
trellis.cpp
trellis.h
userFunctions.cpp
userFunctions.h
viterbi.cpp
weight.cpp
weight.h
stamp-h1
testsuite
TestAlignment
TestCommandline
TestCounting
TestDecoding
TestDecodingALL
TestDiceModelImport
TestDistributions
TestModel
TestModelParsing
TestNewStochHMM
TestSequenceImport
TestStochHMMlib
TestTemplates
TestTraining
TestTrellis
Test_mem_viterbi
usage.h
xcode
StochHMM.xcodeproj
StochHMM
TestTools
Test_newAlphabet
bitwise_ops.cpp
bitwise_ops.h
dynamic_bitset.cpp
dynamic_bitset.h
newStochHMM
sparseArray.h
stateInfo.h