DetermineAlphabet	fn_DetermineAlphabet
SetAlphabet	fn_SetAlphabet
strcpy	fn_strcpy
set_degenerate	fn_set_degenerate
SymbolIndex	fn_SymbolIndex
strchr	fn_strchr
toupper	fn_toupper
DigitizeSequence	fn_DigitizeSequence
DedigitizeSequence	fn_DedigitizeSequence
DigitizeAlignment	fn_DigitizeAlignment
P7CountSymbol	fn_P7CountSymbol
DefaultGeneticCode	fn_DefaultGeneticCode
DefaultCodonBias	fn_DefaultCodonBias
strlen	fn_strlen
CreatePlan7Matrix	fn_CreatePlan7Matrix
ResizePlan7Matrix	fn_ResizePlan7Matrix
AllocPlan7Matrix	fn_AllocPlan7Matrix
FreePlan7Matrix	fn_FreePlan7Matrix
free	fn_free
AllocShadowMatrix	fn_AllocShadowMatrix
FreeShadowMatrix	fn_FreeShadowMatrix
P7ViterbiSize	fn_P7ViterbiSize
P7SmallViterbiSize	fn_P7SmallViterbiSize
P7WeeViterbiSize	fn_P7WeeViterbiSize
P7Forward	fn_P7Forward
P7ViterbiTrace	fn_P7ViterbiTrace
P7SmallViterbi	fn_P7SmallViterbi
P7ParsingViterbi	fn_P7ParsingViterbi
P7WeeViterbi	fn_P7WeeViterbi
Plan7ESTViterbi	fn_Plan7ESTViterbi
P7ViterbiAlignAlignment	fn_P7ViterbiAlignAlignment
ShadowTrace	fn_ShadowTrace
PostprocessSignificantHit	fn_PostprocessSignificantHit
log	fn_log
get_wee_midpt	fn_get_wee_midpt
Statetype	fn_Statetype
AlphabetType2String	fn_AlphabetType2String
P7PrintTrace	fn_P7PrintTrace
fprintf	fn_fprintf
tolower	fn_tolower
fputs	fn_fputs
P7PrintPrior	fn_P7PrintPrior
TraceVerify	fn_TraceVerify
TraceCompare	fn_TraceCompare
DisplayPlan7Posteriors	fn_DisplayPlan7Posteriors
DisplayPlan7PostAlign	fn_DisplayPlan7PostAlign
calloc	fn_calloc
PrintTransition	fn_PrintTransition
DisplayPlan7Matrix	fn_DisplayPlan7Matrix
printf	fn_printf
PrintIscore	fn_PrintIscore
sprintf	fn_sprintf
EmitSequence	fn_EmitSequence
EmitConsensusSequence	fn_EmitConsensusSequence
StateOccupancy	fn_StateOccupancy
WriteProfile	fn_WriteProfile
P7Viterbi	fn_P7Viterbi
AllocHistogram	fn_AllocHistogram
FreeHistogram	fn_FreeHistogram
UnfitHistogram	fn_UnfitHistogram
AddToHistogram	fn_AddToHistogram
floor	fn_floor
PrintASCIIHistogram	fn_PrintASCIIHistogram
PrintXMGRHistogram	fn_PrintXMGRHistogram
ExtremeValueP	fn_ExtremeValueP
PrintXMGRDistribution	fn_PrintXMGRDistribution
PrintXMGRRegressionLine	fn_PrintXMGRRegressionLine
EVDBasicFit	fn_EVDBasicFit
ExtremeValueSetHistogram	fn_ExtremeValueSetHistogram
ExtremeValueFitHistogram	fn_ExtremeValueFitHistogram
EVDDistribution	fn_EVDDistribution
EVDCensoredFit	fn_EVDCensoredFit
EVDMaxLikelyFit	fn_EVDMaxLikelyFit
ExtremeValueE	fn_ExtremeValueE
GaussianFitHistogram	fn_GaussianFitHistogram
sqrt	fn_sqrt
exp	fn_exp
GaussianSetHistogram	fn_GaussianSetHistogram
EVDDensity	fn_EVDDensity
ExtremeValueP2	fn_ExtremeValueP2
EVDrandom	fn_EVDrandom
Lawless416	fn_Lawless416
Lawless422	fn_Lawless422
fabs	fn_fabs
HMMFileOpen	fn_HMMFileOpen
fopen	fn_fopen
fread	fn_fread
HMMFileClose	fn_HMMFileClose
rewind	fn_rewind
fgets	fn_fgets
strncmp	fn_strncmp
HMMFileRead	fn_HMMFileRead
fclose	fn_fclose
HMMFileRewind	fn_HMMFileRewind
HMMFilePositionByName	fn_HMMFilePositionByName
HMMFilePositionByIndex	fn_HMMFilePositionByIndex
WriteAscHMM	fn_WriteAscHMM
WriteBinHMM	fn_WriteBinHMM
fwrite	fn_fwrite
strtok	fn_strtok
feof	fn_feof
fseek	fn_fseek
__ctype_b_loc	fn___ctype_b_loc
atoi	fn_atoi
strcmp	fn_strcmp
atof	fn_atof
strcat	fn_strcat
read_bin20hmm	fn_read_bin20hmm
read_bin19hmm	fn_read_bin19hmm
read_bin17hmm	fn_read_bin17hmm
read_bin11hmm	fn_read_bin11hmm
read_bin10hmm	fn_read_bin10hmm
read_asc20hmm	fn_read_asc20hmm
read_asc19hmm	fn_read_asc19hmm
read_asc17hmm	fn_read_asc17hmm
read_asc11hmm	fn_read_asc11hmm
read_asc10hmm	fn_read_asc10hmm
multiline	fn_multiline
prob2ascii	fn_prob2ascii
write_bin_string	fn_write_bin_string
read_plan9_binhmm	fn_read_plan9_binhmm
byteswap	fn_byteswap
read_plan9_aschmm	fn_read_plan9_aschmm
ascii2prob	fn_ascii2prob
read_bin_string	fn_read_bin_string
hmmcalibrate	fn_hmmcalibrate
time	fn_time
puts	fn_puts
exit	fn_exit
remove	fn_remove
main_loop_serial	fn_main_loop_serial
main	fn_main
main_loop_pvm	fn_main_loop_pvm
main_loop_threaded	fn_main_loop_threaded
main_loop_serial313	fn_main_loop_serial313
Prob2Score	fn_Prob2Score
Score2Prob	fn_Score2Prob
Scorify	fn_Scorify
PValue	fn_PValue
LogSum	fn_LogSum
ILogsum	fn_ILogsum
LogNorm	fn_LogNorm
Logp_cvec	fn_Logp_cvec
SampleDirichlet	fn_SampleDirichlet
SampleGamma	fn_SampleGamma
pow	fn_pow
SampleCountvector	fn_SampleCountvector
P_PvecGivenDirichlet	fn_P_PvecGivenDirichlet
init_ilogsum	fn_init_ilogsum
XNU	fn_XNU
TraceScoreCorrection	fn_TraceScoreCorrection
SantaCruzCorrection	fn_SantaCruzCorrection
HMMERBanner	fn_HMMERBanner
Getword	fn_Getword
Getline	fn_Getline
SetAutocuts	fn_SetAutocuts
P7Handmodelmaker	fn_P7Handmodelmaker
P7Fastmodelmaker	fn_P7Fastmodelmaker
P7Maxmodelmaker	fn_P7Maxmodelmaker
matassign2hmm	fn_matassign2hmm
estimate_model_length	fn_estimate_model_length
build_cij	fn_build_cij
annotate_model	fn_annotate_model
fake_tracebacks	fn_fake_tracebacks
trace_doctor	fn_trace_doctor
AllocPlan7	fn_AllocPlan7
AllocPlan7Shell	fn_AllocPlan7Shell
AllocPlan7Body	fn_AllocPlan7Body
FreePlan7	fn_FreePlan7
ZeroPlan7	fn_ZeroPlan7
Plan7SetName	fn_Plan7SetName
Plan7SetAccession	fn_Plan7SetAccession
Plan7SetDescription	fn_Plan7SetDescription
Plan7ComlogAppend	fn_Plan7ComlogAppend
Plan7SetCtime	fn_Plan7SetCtime
ctime	fn_ctime
Plan7SetNullModel	fn_Plan7SetNullModel
P7Logoddsify	fn_P7Logoddsify
DegenerateSymbolScore	fn_DegenerateSymbolScore
Plan7Renormalize	fn_Plan7Renormalize
Plan7RenormalizeExits	fn_Plan7RenormalizeExits
Plan7NakedConfig	fn_Plan7NakedConfig
Plan7GlobalConfig	fn_Plan7GlobalConfig
Plan7LSConfig	fn_Plan7LSConfig
Plan7SWConfig	fn_Plan7SWConfig
Plan7FSConfig	fn_Plan7FSConfig
Plan7ESTConfig	fn_Plan7ESTConfig
PrintPlan7Stats	fn_PrintPlan7Stats
Plan9toPlan7	fn_Plan9toPlan7
P9AllocHMM	fn_P9AllocHMM
P9ZeroHMM	fn_P9ZeroHMM
P9FreeHMM	fn_P9FreeHMM
P9Renormalize	fn_P9Renormalize
P9DefaultNullModel	fn_P9DefaultNullModel
P7OptimalAccuracy	fn_P7OptimalAccuracy
P7Backward	fn_P7Backward
P7EmitterPosterior	fn_P7EmitterPosterior
P7FillOptimalAccuracy	fn_P7FillOptimalAccuracy
P7OptimalAccuracyTrace	fn_P7OptimalAccuracyTrace
PostalCode	fn_PostalCode
score2postcode	fn_score2postcode
P7AllocPrior	fn_P7AllocPrior
P7FreePrior	fn_P7FreePrior
P7LaplacePrior	fn_P7LaplacePrior
P7DefaultPrior	fn_P7DefaultPrior
P7ReadPrior	fn_P7ReadPrior
PAMPrior	fn_PAMPrior
P7DefaultNullModel	fn_P7DefaultNullModel
P7ReadNullModel	fn_P7ReadNullModel
P7PriorifyHMM	fn_P7PriorifyHMM
P7PriorifyTransitionVector	fn_P7PriorifyTransitionVector
P7PriorifyEmissionVector	fn_P7PriorifyEmissionVector
default_amino_prior	fn_default_amino_prior
default_nucleic_prior	fn_default_nucleic_prior
AllocTophits	fn_AllocTophits
GrowTophits	fn_GrowTophits
FreeTophits	fn_FreeTophits
FreeFancyAli	fn_FreeFancyAli
AllocFancyAli	fn_AllocFancyAli
RegisterHit	fn_RegisterHit
GetRankedHit	fn_GetRankedHit
TophitsMaxName	fn_TophitsMaxName
hit_comparison	fn_hit_comparison
FullSortTophits	fn_FullSortTophits
TophitsReport	fn_TophitsReport
P7AllocTrace	fn_P7AllocTrace
P7ReallocTrace	fn_P7ReallocTrace
P7FreeTrace	fn_P7FreeTrace
TraceSet	fn_TraceSet
MergeTraceArrays	fn_MergeTraceArrays
P7ReverseTrace	fn_P7ReverseTrace
P7TraceCount	fn_P7TraceCount
P7TraceScore	fn_P7TraceScore
TransitionScoreLookup	fn_TransitionScoreLookup
P7Traces2Alignment	fn_P7Traces2Alignment
CreateFancyAli	fn_CreateFancyAli
PrintFancyAli	fn_PrintFancyAli
strncpy	fn_strncpy
fflush	fn_fflush
TraceDecompose	fn_TraceDecompose
TraceDomainNumber	fn_TraceDomainNumber
TraceSimpleBounds	fn_TraceSimpleBounds
MasterTraceFromMap	fn_MasterTraceFromMap
ImposeMasterTrace	fn_ImposeMasterTrace
rightjustify	fn_rightjustify
specqsort	fn_specqsort
qst	fn_qst
ReadA2M	fn_ReadA2M
WriteA2M	fn_WriteA2M
ComparePairAlignments	fn_ComparePairAlignments
CompareRefPairAlignments	fn_CompareRefPairAlignments
CompareMultAlignments	fn_CompareMultAlignments
CompareRefMultAlignments	fn_CompareRefMultAlignments
PairwiseIdentity	fn_PairwiseIdentity
AlignmentIdentityBySampling	fn_AlignmentIdentityBySampling
MajorityRuleConsensus	fn_MajorityRuleConsensus
make_alilist	fn_make_alilist
compare_lists	fn_compare_lists
make_ref_alilist	fn_make_ref_alilist
AllocAlignment	fn_AllocAlignment
InitAinfo	fn_InitAinfo
FreeAlignment	fn_FreeAlignment
SAMizeAlignment	fn_SAMizeAlignment
SAMizeAlignmentByGapFrac	fn_SAMizeAlignmentByGapFrac
MakeAlignedString	fn_MakeAlignedString
MakeDealignedString	fn_MakeDealignedString
DealignedLength	fn_DealignedLength
WritePairwiseAlignment	fn_WritePairwiseAlignment
MingapAlignment	fn_MingapAlignment
RandomAlignment	fn_RandomAlignment
AlignmentHomogenousGapsym	fn_AlignmentHomogenousGapsym
ReadClustal	fn_ReadClustal
strstr	fn_strstr
strpbrk	fn_strpbrk
WriteClustal	fn_WriteClustal
Cluster	fn_Cluster
AllocPhylo	fn_AllocPhylo
malloc	fn_malloc
FreePhylo	fn_FreePhylo
MakeDiffMx	fn_MakeDiffMx
MakeIdentityMx	fn_MakeIdentityMx
PrintNewHampshireTree	fn_PrintNewHampshireTree
PrintPhylo	fn_PrintPhylo
ParsePAMFile	fn_ParsePAMFile
strrchr	fn_strrchr
EPSWriteSmallMSA	fn_EPSWriteSmallMSA
FileDirname	fn_FileDirname
FileTail	fn_FileTail
FileSameDirectory	fn_FileSameDirectory
FileConcat	fn_FileConcat
FileAddSuffix	fn_FileAddSuffix
EnvFileOpen	fn_EnvFileOpen
getenv	fn_getenv
FileExists	fn_FileExists
Getopt	fn_Getopt
GKIInit	fn_GKIInit
GKIFree	fn_GKIFree
GKIStoreKey	fn_GKIStoreKey
GKIKeyIndex	fn_GKIKeyIndex
GKIStatus	fn_GKIStatus
gki_alloc	fn_gki_alloc
gki_hashvalue	fn_gki_hashvalue
gki_upsize	fn_gki_upsize
GSIOpen	fn_GSIOpen
GSIGetRecord	fn_GSIGetRecord
GSIGetOffset	fn_GSIGetOffset
GSIClose	fn_GSIClose
GSIAllocIndex	fn_GSIAllocIndex
GSIFreeIndex	fn_GSIFreeIndex
GSIAddFileToIndex	fn_GSIAddFileToIndex
GSIAddKeyToIndex	fn_GSIAddKeyToIndex
GSISortIndex	fn_GSISortIndex
GSIWriteIndex	fn_GSIWriteIndex
GSIWriteHeader	fn_GSIWriteHeader
GSIWriteFileRecord	fn_GSIWriteFileRecord
GSIWriteKeyRecord	fn_GSIWriteKeyRecord
gsi_keysorter	fn_gsi_keysorter
Strparse	fn_Strparse
sqd_regcomp	fn_sqd_regcomp
sqd_regexec	fn_sqd_regexec
SqdClean	fn_SqdClean
sqd_regerror	fn_sqd_regerror
sqd_regsub	fn_sqd_regsub
strspn	fn_strspn
strcspn	fn_strcspn
regc	fn_regc
reg	fn_reg
regnext	fn_regnext
regtry	fn_regtry
regmatch	fn_regmatch
regrepeat	fn_regrepeat
regoptail	fn_regoptail
regtail	fn_regtail
regbranch	fn_regbranch
regpiece	fn_regpiece
reginsert	fn_reginsert
regatom	fn_regatom
regnode	fn_regnode
MSAAlloc	fn_MSAAlloc
MSAExpand	fn_MSAExpand
MSAFree	fn_MSAFree
MSASetSeqAccession	fn_MSASetSeqAccession
MSASetSeqDescription	fn_MSASetSeqDescription
MSAAddComment	fn_MSAAddComment
MSAAddGF	fn_MSAAddGF
MSAAddGS	fn_MSAAddGS
MSAAppendGC	fn_MSAAppendGC
MSAGetGC	fn_MSAGetGC
MSAAppendGR	fn_MSAAppendGR
MSAVerifyParse	fn_MSAVerifyParse
MSAFileOpen	fn_MSAFileOpen
MSAFileFormat	fn_MSAFileFormat
MSAFileRewind	fn_MSAFileRewind
MSAFilePositionByKey	fn_MSAFilePositionByKey
MSAFilePositionByIndex	fn_MSAFilePositionByIndex
MSAFileRead	fn_MSAFileRead
MSAFileClose	fn_MSAFileClose
MSAFileGetLine	fn_MSAFileGetLine
MSAFileWrite	fn_MSAFileWrite
MSAGetSeqidx	fn_MSAGetSeqidx
MSAFromAINFO	fn_MSAFromAINFO
MSAMingap	fn_MSAMingap
MSAShorterAlignment	fn_MSAShorterAlignment
MSANogap	fn_MSANogap
MSASmallerAlignment	fn_MSASmallerAlignment
MSAGetSeqAccession	fn_MSAGetSeqAccession
MSAGetSeqDescription	fn_MSAGetSeqDescription
MSAGetSeqSS	fn_MSAGetSeqSS
MSAGetSeqSA	fn_MSAGetSeqSA
MSAAverageSequenceLength	fn_MSAAverageSequenceLength
ReadMSF	fn_ReadMSF
WriteMSF	fn_WriteMSF
strftime	fn_strftime
localtime	fn_localtime
fputc	fn_fputc
ReadPhylip	fn_ReadPhylip
WritePhylip	fn_WritePhylip
revcomp	fn_revcomp
rkcomp	fn_rkcomp
rkseq	fn_rkseq
ReadSELEX	fn_ReadSELEX
WriteSELEX	fn_WriteSELEX
WriteSELEXOneBlock	fn_WriteSELEXOneBlock
DealignAseqs	fn_DealignAseqs
IsSELEXFormat	fn_IsSELEXFormat
copy_alignment_line	fn_copy_alignment_line
actually_write_selex	fn_actually_write_selex
seqcmp	fn_seqcmp
seqncmp	fn_seqncmp
seqencode	fn_seqencode
coded_revcomp	fn_coded_revcomp
seqdecode	fn_seqdecode
seqndecode	fn_seqndecode
StrShuffle	fn_StrShuffle
StrDPShuffle	fn_StrDPShuffle
StrMarkov0	fn_StrMarkov0
StrMarkov1	fn_StrMarkov1
StrReverse	fn_StrReverse
StrRegionalShuffle	fn_StrRegionalShuffle
AlignmentShuffle	fn_AlignmentShuffle
AlignmentBootstrap	fn_AlignmentBootstrap
QRNAShuffle	fn_QRNAShuffle
Die	fn_Die
vfprintf	fn_vfprintf
Warn	fn_Warn
Panic	fn_Panic
perror	fn_perror
SeqfileOpen	fn_SeqfileOpen
SeqfileOpenForIndexing	fn_SeqfileOpenForIndexing
SeqfilePosition	fn_SeqfilePosition
SeqfileRewind	fn_SeqfileRewind
SeqfileLineParameters	fn_SeqfileLineParameters
SeqfileClose	fn_SeqfileClose
FreeSequence	fn_FreeSequence
SetSeqinfoString	fn_SetSeqinfoString
strncat	fn_strncat
SeqinfoCopy	fn_SeqinfoCopy
ToDNA	fn_ToDNA
ToRNA	fn_ToRNA
ToIUPAC	fn_ToIUPAC
ReadSeq	fn_ReadSeq
SeqfileFormat	fn_SeqfileFormat
Seqtype	fn_Seqtype
GCGBinaryToSequence	fn_GCGBinaryToSequence
GCGchecksum	fn_GCGchecksum
GCGMultchecksum	fn_GCGMultchecksum
GuessAlignmentSeqtype	fn_GuessAlignmentSeqtype
WriteSimpleFASTA	fn_WriteSimpleFASTA
WriteSeq	fn_WriteSeq
ReadMultipleRseqs	fn_ReadMultipleRseqs
String2SeqfileFormat	fn_String2SeqfileFormat
SeqfileFormat2String	fn_SeqfileFormat2String
MSAToSqinfo	fn_MSAToSqinfo
realloc	fn_realloc
seqfile_open	fn_seqfile_open
SeqfileGetLine	fn_SeqfileGetLine
readIG	fn_readIG
readStrider	fn_readStrider
readGenBank	fn_readGenBank
readPearson	fn_readPearson
readEMBL	fn_readEMBL
readZuker	fn_readZuker
readPIR	fn_readPIR
readGCGdata	fn_readGCGdata
readUWGCG	fn_readUWGCG
addseq	fn_addseq
endGCGdata	fn_endGCGdata
readLoop	fn_readLoop
endPIR	fn_endPIR
endZuker	fn_endZuker
endEMBL	fn_endEMBL
endPearson	fn_endPearson
endGB	fn_endGB
endStrider	fn_endStrider
endIG	fn_endIG
SqdBanner	fn_SqdBanner
sre_tolower	fn_sre_tolower
sre_toupper	fn_sre_toupper
Linefit	fn_Linefit
WeightedLinefit	fn_WeightedLinefit
Gammln	fn_Gammln
FMX2Alloc	fn_FMX2Alloc
FMX2Free	fn_FMX2Free
DMX2Alloc	fn_DMX2Alloc
DMX2Free	fn_DMX2Free
FMX2Multiply	fn_FMX2Multiply
IncompleteGamma	fn_IncompleteGamma
sre_random	fn_sre_random
sre_srandom	fn_sre_srandom
sre_random_positive	fn_sre_random_positive
ExponentialRandom	fn_ExponentialRandom
Gaussrandom	fn_Gaussrandom
DChoose	fn_DChoose
FChoose	fn_FChoose
Strdup	fn_Strdup
StringChop	fn_StringChop
Strinsert	fn_Strinsert
Strdelete	fn_Strdelete
s2lower	fn_s2lower
s2upper	fn_s2upper
sre_malloc	fn_sre_malloc
sre_realloc	fn_sre_realloc
Free2DArray	fn_Free2DArray
Free3DArray	fn_Free3DArray
RandomSequence	fn_RandomSequence
sre_fgets	fn_sre_fgets
sre_strcat	fn_sre_strcat
sre_strtok	fn_sre_strtok
sre_strdup	fn_sre_strdup
sre_strncpy	fn_sre_strncpy
IsBlankline	fn_IsBlankline
SSIOpen	fn_SSIOpen
SSIGetOffsetByName	fn_SSIGetOffsetByName
SSIGetOffsetByNumber	fn_SSIGetOffsetByNumber
SSIGetSubseqOffset	fn_SSIGetSubseqOffset
SSISetFilePosition	fn_SSISetFilePosition
SSIFileInfo	fn_SSIFileInfo
SSIClose	fn_SSIClose
SSIRecommendMode	fn_SSIRecommendMode
SSICreateIndex	fn_SSICreateIndex
SSIFreeIndex	fn_SSIFreeIndex
SSIGetFilePosition	fn_SSIGetFilePosition
ftell	fn_ftell
abort	fn_abort
SSIAddFileToIndex	fn_SSIAddFileToIndex
SSISetFileForSubseq	fn_SSISetFileForSubseq
SSIAddPrimaryKeyToIndex	fn_SSIAddPrimaryKeyToIndex
SSIAddSecondaryKeyToIndex	fn_SSIAddSecondaryKeyToIndex
SSIWriteIndex	fn_SSIWriteIndex
system	fn_system
SSIErrorString	fn_SSIErrorString
SSIForceExternalSort	fn_SSIForceExternalSort
strtoul	fn_strtoul
load_indexfile	fn_load_indexfile
binary_search	fn_binary_search
read_i16	fn_read_i16
read_offset	fn_read_offset
indexfile_position	fn_indexfile_position
read_i32	fn_read_i32
clear_ssifile	fn_clear_ssifile
current_index_size	fn_current_index_size
activate_external_sort	fn_activate_external_sort
pkeysort	fn_pkeysort
skeysort	fn_skeysort
write_i32	fn_write_i32
write_i16	fn_write_i16
write_i64	fn_write_i64
parse_pkey_info	fn_parse_pkey_info
write_offset	fn_write_offset
parse_skey_info	fn_parse_skey_info
read_i64	fn_read_i64
InitIntStack	fn_InitIntStack
PushIntStack	fn_PushIntStack
PopIntStack	fn_PopIntStack
ReverseIntStack	fn_ReverseIntStack
FreeIntStack	fn_FreeIntStack
ReadStockholm	fn_ReadStockholm
WriteStockholm	fn_WriteStockholm
WriteStockholmOneBlock	fn_WriteStockholmOneBlock
parse_gf	fn_parse_gf
parse_gs	fn_parse_gs
parse_gc	fn_parse_gc
parse_gr	fn_parse_gr
parse_comment	fn_parse_comment
parse_sequence	fn_parse_sequence
actually_write_stockholm	fn_actually_write_stockholm
Translate	fn_Translate
IsInt	fn_IsInt
IsReal	fn_IsReal
Byteswap	fn_Byteswap
sre_ntoh16	fn_sre_ntoh16
sre_ntoh32	fn_sre_ntoh32
sre_hton16	fn_sre_hton16
sre_hton32	fn_sre_hton32
sre_ntoh64	fn_sre_ntoh64
sre_hton64	fn_sre_hton64
DSet	fn_DSet
FSet	fn_FSet
DScale	fn_DScale
FScale	fn_FScale
DSum	fn_DSum
FSum	fn_FSum
DAdd	fn_DAdd
FAdd	fn_FAdd
DCopy	fn_DCopy
FCopy	fn_FCopy
DDot	fn_DDot
FDot	fn_FDot
DMax	fn_DMax
FMax	fn_FMax
DMin	fn_DMin
FMin	fn_FMin
DArgMax	fn_DArgMax
FArgMax	fn_FArgMax
DArgMin	fn_DArgMin
FArgMin	fn_FArgMin
DNorm	fn_DNorm
FNorm	fn_FNorm
DLog	fn_DLog
FLog	fn_FLog
DExp	fn_DExp
FExp	fn_FExp
DLogSum	fn_DLogSum
FLogSum	fn_FLogSum
GSCWeights	fn_GSCWeights
VoronoiWeights	fn_VoronoiWeights
BlosumWeights	fn_BlosumWeights
SingleLinkCluster	fn_SingleLinkCluster
PositionBasedWeights	fn_PositionBasedWeights
FilterAlignment	fn_FilterAlignment
SampleAlignment	fn_SampleAlignment
upweight	fn_upweight
downweight	fn_downweight
simple_diffmx	fn_simple_diffmx
simple_distance	fn_simple_distance
