activeblocks
addClusterEdge
adddistribution
adddistributionUint64
addmultidistribution
addmultidistributionUint64
addmultiseq
addoption
addspace
addunsortedrange
alignequalstrings
alignlinearspace
allocandusespaceviaptr
applyall
applyallasize
applymatchcontainer
assignDNAalphabet
assignProteinalphabet
besesuffixsort
besesuffixsortspecial
binlcpvalue
binsearch
binsearchPairUint
binsearchstring
bmhcheck
bmhcount
bmhout
breadthfirstvstree
bruteforchainingwithcounts
bucketsortsuffixes
bwtdecode
bwtdecode2
bytecode2string
calculateseqparm
calculatetwolongestseqlength
calledistunit
callgenericextend
callmkvtree
callmkvtreegeneric
ceillog2
checkdoubleexclude
checkenvvaronoff
checkexactcompletematchesindex
checkexactcompletematchesonline
checkexclude
checkfilehandles
checkforsingleexcludeoption
checkgzipsuffix
checkifvstreetabfileexists
checkleafblocktree
checkshowstringmultiple
checksortmode
checkspaceleak
checksufencoding
checktransnum
closeesastream
closegenericstream
clusterSizedistribution
cmpEvaluetype
cmpmaxdist
cmpmaxdistgeneric
compareAlphabet
compareleafblocktrees
compareSinttab
compareUchartab
compareUinttab
completevirtualtree
composefilename
compresscldtab
computeofflineexactmatches
concatmanyfiles
concatsorthelp
concatsortmodes
constructvirtualtreetables
containswildcard
copyAlphabet
copyfilenamesofMultiseq
copyMultiseq
copymultiseqRC
copymultiseqRCorig
createfilehandle
creatememorymap
creatememorymapforfiledesc
createtistabmap
decodeburrowswheeler
decodeburrowswheelerspecial
deletefilehandle
deleteheadofqueue
deletememorymap
deletesmallestpath
dequeue
dequeuegeneric
destroyleafblocktree
determineAlphabet
determine_eop_length
determine_eop_type
distanceofstrings
distboundarycases
echoexactmatch
echothedescription
edistprocessstartpos
editextend
emptyqueuegeneric
encodeburrowswheeler
encseqtable2seqoffsets
enqueue
enqueuegeneric
enumvleaves
enumvnodes
esaapm
esahamming
evaleditxdropleft
evaleditxdropright
evalhammingxdropleft
evalhammingxdropright
evaluatedistanceoflongstrings
evalxdroptableleft
evalxdroptableright
extendedleftSEP
extendedrightSEP
extractaminoacid
extractindexname
extractoption
extractoptionwithpossibleargument
extractprefixbytecode
extractrootkey
fancyformatting
fastchaining
file2lines
filealreadyexists
fillscorematrix
fillthethreealignmentlines
fillthetwoalignmentlines
findabspos
findalphabet
findapproxcompletematchesindex
findboundaries
findcharintervalbin
findcompletematches
findedistcompletematchesindex
findedistcompletematchesonline
findexactcompletematchescompressedindex
findexactcompletematchesindex
findexactcompletematchesonline
findfirstpos
findhammingcompletematchesindex
findhammingcompletematchesonline
findmaximaluniquematches
findmaxprefixlen
findmaxprefixlenstack
findparentinterval
findquerymatches
findselfmatches
findsiblings
findsmallestnodeintrie
findstartcodon
findsupermax
findtandems
findunitboundaries
findunitfirstpos
formatseq
freebestmatchlist
freeblastmatrix
freeClusterSet
freeDPbitvectorreservoir
freeEncodedsequence
freeEvalues
freemultiseq
freemultiseqfileinfo
freespaceviaptr
freetrierep
freevirtualtree
freevirtualtreemain
genclose
gengetc
genopen
genprintf
genputc
getclockticks
getdirname
getEqs4
getEqs8
getEqsrev4
getEqsrev8
geterror
getEvalue
getexception
getfasta
getfastastream
getfilenum
getoriginal
getqueryseppos
getrecordnum
getredblacktreespacepeak
getruntime
getseqinfo
getseqnum
getspacepeak
getunitinfo
greedyedistalign
groupmatchesbyseqnum
guessifproteinsequence
hammingalignment
hammingextend
hammingprocessstartpos
headofqueue
headofqueuegeneric
helptransnumorganism
huffmanencoding
incgetEvalue
incprecomputehammingEvalues
initbml
initclock
initClusterSet
initcompletematchstruct
initDictmaxsize
initDPbitvectorreservoir
initEmissionmergedesa
initencodedseq
initesastream
initgreedyalignreservoir
initgreedyextendreservoir
inithammingEvalues
initleafblocktree
initmaintainedfragments
initmappower
initMatchstate
initmkvaux
initmkvauxspecial
initmultiseq
initmultiseqfileinfo
initmulttab
initoptions
initpminfo
initRmnsufinfo
inittmpfiledesc
inittrienodetable
initUcharBufferedfile
insertDictmaxsize
insertintobml
insertnewregion
insertsuffixintotrie
intbits2string
integercode2string
isbranching
isinsingleton
islittleendian
karlinunitcostpp
kmercode2string
leafblocktreememreposfree
leafblocktreememreposinit
lengthdistribution
linkcluster
localbese
localsimilarityregion
localsimilarityscore
longpatternlongestmatch
makeemptyvirtualtree
makeindexfilecopy
makereversecomplement
makereversecomplementorig
makeskiptable
maketmpfile
mapallofvirtualtreewhatsthere
mapalphabetifyoucan
mapandparsepossiblygzippedfastafile
mapandparsesequencefile
mapmultiseqifyoucan
mapskptab
mapvirtualtreeifyoucan
matchcontainer
matchquerysubstring0
matchquerysubstring1
matchquerysubstring2
matchquerysubstring3
matchquerysubstring4
matchquerysubstring5
matchvirtagainstvirt
matchvirtagainstvirt2
matchvirtagainstvirt3
maxerrormsg
maximalDPedges
maximumlinelength
maxprefixmatch2
maxprefixmatchbinstep
maxprefixmatchbinstepwithprevious
maxprefixmatchmm
mediumpatternlongestmatch
mergeleafblocktrees
messagespace
mkcldtabnextlIndex
mkcldtabupdown
mkvtreeinput
mkvtreeprocess
mmcheckspaceleak
mmgetspacepeak
mmsearch
mmshowspace
multiseqonlycomplement
multiseqreverse
multiseqreversecomplement
multisixframetranslateDNA
mumuniqueinquery
onexdropalignment1
onexdropalignment2
onlycomplement
opengenericstream
optionaddbitmask
outindextab
outputUintvalue
outrubytranstable
overalloriginalsequences
overallpairsofsequences
overallqueuelements
overallqueuelementsgeneric
overallsequences
parseMultiformat
parseprojectfile
parsequalifiedinteger
pos2pospair
precomputehammingEvalues
prepareforsixframeselfmatch
processexactquerymatch
processnewquhit
processsequence
procoption
producealignment
produceqhits
produceqhitsimple
pumpthroughcache
qsortPairUintwrtuint0
qsortStorematchbydiagonal
qsortThreeUintwrtuint2
qsortUint
queueisempty
queueisemptygeneric
readblastmatrix
readblastmatrixgeneric
readencodedseq
readfromfilehandle
readgzippedfile
readmultiplefastafile
readmultiplefastafileagain
readmultiplefastafilesep
readmultiseq
readmultiseqagain
readnextline
readsymbolmap
recommendedmaxlevel
recomputevirtualtreemarkpos
redblacktreedelete
redblacktreedestroy
redblacktreefind
redblacktreemaximumkey
redblacktreeminimumkey
redblacktreenextequalkey
redblacktreenextkey
redblacktreepreviousequalkey
redblacktreepreviouskey
redblacktreesearch
redblacktreewalk
redblacktreewalkrange
redblacktreewalkreverseorder
redblacktreewalkwithstop
remdups
removecontained
removeexistingindex
removeexistingindexfile
reportmaximalpairs
reseterror
reverseAlignment
reversecomplement
reversecomplementinplace
reverseinplace
reversestring
rewindgenericstream
safecasttoSint
safecasttoUint
safestringcopy
scanpathsforfile
searchpattern
searchpatternapprox
searchpatterngeneric
seqnum2filenum
seterror
shiftbytecode
shortpatternlongestmatch
showalignment
showalignmentgeneric
showalignmentprotein
showblastmatrix
showClusterSet
showdescandlength
showdevoptions
showdistribution
showdistribution_generic
showeditops
showeditopsgeneric
showexclude
showmultiplefasta
showonednaorproteineditop
showoneeditop
showoptions
showoptionsinlatex
showoptionsinlatexwithoutdevoptions
showoptionswithoutdevoptions
showoptionswithoutexclude
showoptionswithoutexcludeandwithoutdevoptions
showprogramversion
showscoredistribution
showSingletonSet
showSortedList
showspace
showStoreMatch
showsuperbck
showsymbolmap
showvirtualtreestatus
showvirtualtreestatusonstdout
significance
simplebck2superbck
simplefileOpen
singlesixframetranslateDNA
sixframeconvertmatch
sizeofgenericqueue
skiplistcurrentnext
skiplistdelete
skiplistdestroy
skiplistexternalfingernextequalkey
skiplistexternalfingernextequalkeywithmacro
skiplistexternalfingernextequalkeywithmacro2
skiplistexternalfingernextkey
skiplistfind
skiplistfingernextequalkey
skiplistfingernextkey
skiplistfreeexternalfinger
skiplistinit
skiplistinitexternalfinger
skiplistinitfinger
skiplistinitwithkey
skiplistinsert
skiplistmerge
skiplistminimumkey
skiplistnextequalkey
skiplistnextkey
skiplistprint
skiplistprintvalues
skipliststatistics
skiplistwalk
smithwatermanDP
sortallmatches
spaceblockinfo
splitargstring
splitesaapm
splitnodewithcharbin
splitnodewithcharbinwithoutspecial
stepdeleteandinsertothersuffixes
string2bytecode
string2bytecodewithspecial
string2uint
strmvmatmaxoutdynamic
subtractspace
tailofqueue
tracebackDPedges
transformstring
transformstringincopy
translateDNAbackward
translateDNAforward
transnum2name
transsuftab
treeshape
turnwheels
undefsortmode
unitedistfrontSEPgeneric
verbosealphabet
verbosealphachar
verifyregiontree
verifysuffixofindexname
vgenprintf
virtual2tex
vmatmaxcount12
vmatmaxcount21
vmatmaxcount31
vmatmaxcount4
vmatmaxcount42
vmatmaxcount53
vmatmaxcount66
vmatmaxcountgeneric
vmatmaxout12
vmatmaxout21
vmatmaxout31
vmatmaxout4
vmatmaxout42
vmatmaxout53
vmatmaxout66
vmatmaxoutdynamic
vmatmaxoutgeneric
vmatmaxoutwithgaps
vm_checkprefixlength
vm_determinenumofcodes
vm_dynamicstrdup
vm_getbasename
vm_guessifproteinsequencestream
vm_isdnaalphabet
vm_isproteinalphabet
vm_recommendedprefixlength
vm_showmaximalprefixlength
vm_showsymbolstring
vm_showsymbolstringgeneric
vm_whatisthemaximalprefixlength
wrapgreedyextendreservoir
wrapmaintainedfragments
wrapqueue
wrapqueuegeneric
wrapRmnsufinfo
wraptEmissionmergedesa
wraptgreedyalignreservoir
wraptmpfiledesc
writetofilehandle
xdropseedextend
