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Scripts and libraries to perform motif searches inside genomes

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mgalardinimgalardini
regHMM: pairwise comparisons
Mar 11, 2015
c43ea2b · Mar 11, 2015

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regtools
regtools
 
 
utils
utils
 
 
README.md
README.md
 
 
alignCore
alignCore
 
 
analyzeHits
analyzeHits
 
 
autoBiopy
autoBiopy
 
 
autoHMM
autoHMM
 
 
autoMast
autoMast
 
 
autoParallelBiopy
autoParallelBiopy
 
 
autoParams
autoParams
 
 
autoParamsTable
autoParamsTable
 
 
autoRSAT
autoRSAT
 
 
chk2Dists
chk2Dists
 
 
combineDists
combineDists
 
 
compareLiterature
compareLiterature
 
 
concateAlign
concateAlign
 
 
copyResults
copyResults
 
 
countHits
countHits
 
 
dispDist
dispDist
 
 
doBfile
doBfile
 
 
doBiopy
doBiopy
 
 
doCOGTable
doCOGTable
 
 
doGenomicDist
doGenomicDist
 
 
doGenomicDist_3.2
doGenomicDist_3.2
 
 
doHMM
doHMM
 
 
doHMMbuild
doHMMbuild
 
 
doMantel
doMantel
 
 
doMast
doMast
 
 
doOfs
doOfs
 
 
doParallelBiopy
doParallelBiopy
 
 
doRSAT
doRSAT
 
 
echoRSAT
echoRSAT
 
 
fasta2Nexus
fasta2Nexus
 
 
filterUpstream
filterUpstream
 
 
fixNexus
fixNexus
 
 
gbk2fna
gbk2fna
 
 
genomeStats
genomeStats
 
 
get16S
get16S
 
 
getAlignments
getAlignments
 
 
getAllDownstream
getAllDownstream
 
 
getDownstream
getDownstream
 
 
getIGS
getIGS
 
 
getIGSfromGFF
getIGSfromGFF
 
 
getLocus
getLocus
 
 
getMastEvalue
getMastEvalue
 
 
getRegLoc
getRegLoc
 
 
getRegRep
getRegRep
 
 
getRsatEvalue
getRsatEvalue
 
 
getScores
getScores
 
 
getThreshold
getThreshold
 
 
get_replicons.sh
get_replicons.sh
 
 
grepGO
grepGO
 
 
isNorm
isNorm
 
 
list_genbank_id.sh
list_genbank_id.sh
 
 
mapContigs
mapContigs
 
 
mergeMethods
mergeMethods
 
 
mergeMotifs
mergeMotifs
 
 
motifParams
motifParams
 
 
mrBayes2Newick
mrBayes2Newick
 
 
mrBayes2Newick_3.2
mrBayes2Newick_3.2
 
 
nexus2MrBayes
nexus2MrBayes
 
 
op2tab
op2tab
 
 
orgNet
orgNet
 
 
pangenomeNet
pangenomeNet
 
 
parallelBiopy
parallelBiopy
 
 
parseBiopy
parseBiopy
 
 
parseCOG
parseCOG
 
 
parseContigs
parseContigs
 
 
parseHMM
parseHMM
 
 
parseMast
parseMast
 
 
parseRSAT
parseRSAT
 
 
parseScores
parseScores
 
 
plotDist
plotDist
 
 
plotGeneHits
plotGeneHits
 
 
plotMethodDist
plotMethodDist
 
 
regCore
regCore
 
 
regDist
regDist
 
 
regHMM
regHMM
 
 
regList
regList
 
 
regRapresentative
regRapresentative
 
 
regStats
regStats
 
 
regTransitions
regTransitions
 
 
runCompare
runCompare
 
 
runDownstream
runDownstream
 
 
searchBiopy
searchBiopy
 
 
splitScaffold
splitScaffold
 
 
treeDist
treeDist
 
 
upstreamGetter
upstreamGetter
 
 

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regtools

Scripts and libraries to perform motif searches inside genomes

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Scripts and libraries to perform motif searches inside genomes

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