Index

Symbols

--1f <fields_1> PairSeq command line option --1f <head_fields> AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option --2f <fields_2> PairSeq command line option --2f <tail_fields> AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option --act {min,max,sum,first,last,set,cat} ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-rename command line option --act {min,max,sum,set,majority} BuildConsensus command line option --act {min,max,sum,set} CollapseSeq command line option --alpha <alpha> AssemblePairs-align command line option --barcode MaskPrimers-align command line option MaskPrimers-score command line option --bf <barcode_field> AlignSets-muscle command line option AlignSets-offset command line option BuildConsensus command line option --cf <copy_fields> BuildConsensus command line option CollapseSeq command line option --coord {illumina,solexa,sra,454,presto} AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option PairSeq command line option SplitSeq-samplepair command line option --delim <delimiter> AlignSets-muscle command line option AlignSets-offset command line option AlignSets-table command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option EstimateError command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option ParseLog command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option --dep BuildConsensus command line option --div AlignSets-muscle command line option AlignSets-offset command line option --end <seq_end> ClusterSets command line option --evalue <evalue> AssemblePairs-reference command line option --exec <muscle_exec> AlignSets-muscle command line option AlignSets-table command line option --exec <usearch_exec> AssemblePairs-reference command line option ClusterSets command line option --failed AlignSets-muscle command line option AlignSets-offset command line option AlignSets-table command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option --fasta AlignSets-muscle command line option AlignSets-offset command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option SplitSeq-count command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option --fill AssemblePairs-reference command line option --freq <min_freq> BuildConsensus command line option EstimateError command line option --gap <gap> AssemblePairs-join command line option --gap <gap_penalty> MaskPrimers-align command line option --id <ident> ClusterSets command line option --inner CollapseSeq command line option FilterSeq-length command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option --keepmiss CollapseSeq command line option --log <log_file> AlignSets-muscle command line option AlignSets-offset command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option EstimateError command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option --maxdiv <max_diversity> BuildConsensus command line option EstimateError command line option --maxerror <max_error> AssemblePairs-align command line option BuildConsensus command line option MaskPrimers-align command line option MaskPrimers-score command line option --maxf <max_field> CollapseSeq command line option --maxgap <max_gap> BuildConsensus command line option --maxhits <max_hits> AssemblePairs-reference command line option --maxlen <max_len> AssemblePairs-align command line option MaskPrimers-align command line option --minf <min_field> CollapseSeq command line option --minident <min_ident> AssemblePairs-reference command line option --minlen <min_len> AssemblePairs-align command line option --missing FilterSeq-repeats command line option --mode {cut,mask,trim,tag} MaskPrimers-align command line option MaskPrimers-score command line option --mode {freq,qual} EstimateError command line option

--mode {pad,cut} AlignSets-offset command line option --nproc <nproc> AlignSets-muscle command line option AlignSets-offset command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option EstimateError command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option --num SplitSeq-sort command line option --num <threshold> SplitSeq-group command line option --outdir <out_dir> AlignSets-muscle command line option AlignSets-offset command line option AlignSets-table command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option EstimateError command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option ParseLog command line option SplitSeq-count command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option --outname <out_name> AlignSets-muscle command line option AlignSets-offset command line option AlignSets-table command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option EstimateError command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option ParseLog command line option SplitSeq-count command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option --pf <primer_field> AlignSets-offset command line option BuildConsensus command line option --prcons <primer_freq> BuildConsensus command line option --rc {head,tail,both} AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option --reverse AlignSets-table command line option FilterSeq-trimqual command line option --revpr MaskPrimers-align command line option MaskPrimers-score command line option --scanrev AssemblePairs-align command line option --sep <separator> ParseHeaders-expand command line option --simple ConvertHeaders-imgt command line option --skiprc MaskPrimers-align command line option --start <seq_start> ClusterSets command line option --start <start> MaskPrimers-score command line option --uf <uniq_fields> CollapseSeq command line option --version AlignSets command line option AssemblePairs command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders command line option EstimateError command line option FilterSeq command line option MaskPrimers command line option PairSeq command line option ParseHeaders command line option ParseLog command line option SplitSeq command line option --win <window> FilterSeq-trimqual command line option -1 <seq_files_1> AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option PairSeq command line option SplitSeq-samplepair command line option -2 <seq_files_2> AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option PairSeq command line option SplitSeq-samplepair command line option -d <offset_table> AlignSets-offset command line option -f <barcode_field> ClusterSets command line option -f <field> SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option -f <fields> ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option ParseLog command line option -f <set_field> EstimateError command line option -h, --help AlignSets command line option AlignSets-muscle command line option AlignSets-offset command line option AlignSets-table command line option AssemblePairs command line option AssemblePairs-align command line option AssemblePairs-join command line option AssemblePairs-reference command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option EstimateError command line option FilterSeq command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers command line option MaskPrimers-align command line option MaskPrimers-score command line option PairSeq command line option ParseHeaders command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option ParseLog command line option SplitSeq command line option SplitSeq-count command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option -k <cluster_field> ClusterSets command line option -k <names> ParseHeaders-copy command line option ParseHeaders-rename command line option -l <record_files> ParseLog command line option -n <max_count> SplitSeq-count command line option SplitSeq-sample command line option SplitSeq-samplepair command line option SplitSeq-sort command line option -n <max_missing> CollapseSeq command line option FilterSeq-missing command line option -n <max_repeat> FilterSeq-repeats command line option -n <min_count> BuildConsensus command line option EstimateError command line option -n <min_length> FilterSeq-length command line option -p <primer_file> AlignSets-table command line option MaskPrimers-align command line option MaskPrimers-score command line option -q <min_qual> BuildConsensus command line option EstimateError command line option FilterSeq-maskqual command line option FilterSeq-quality command line option FilterSeq-trimqual command line option -r <ref_file> AssemblePairs-reference command line option -s <seq_files> AlignSets-muscle command line option AlignSets-offset command line option BuildConsensus command line option ClusterSets command line option CollapseSeq command line option ConvertHeaders-454 command line option ConvertHeaders-genbank command line option ConvertHeaders-generic command line option ConvertHeaders-illumina command line option ConvertHeaders-imgt command line option ConvertHeaders-sra command line option EstimateError command line option FilterSeq-length command line option FilterSeq-maskqual command line option FilterSeq-missing command line option FilterSeq-quality command line option FilterSeq-repeats command line option FilterSeq-trimqual command line option MaskPrimers-align command line option MaskPrimers-score command line option ParseHeaders-add command line option ParseHeaders-collapse command line option ParseHeaders-copy command line option ParseHeaders-delete command line option ParseHeaders-expand command line option ParseHeaders-rename command line option ParseHeaders-table command line option SplitSeq-count command line option SplitSeq-group command line option SplitSeq-sample command line option SplitSeq-sort command line option -u <values> ParseHeaders-add command line option SplitSeq-sample command line option SplitSeq-samplepair command line option

A

AlignSets command line option --version -h, --help AlignSets-muscle command line option --bf <barcode_field> --delim <delimiter> --div --exec <muscle_exec> --failed --fasta --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> AlignSets-offset command line option --bf <barcode_field> --delim <delimiter> --div --failed --fasta --log <log_file> --mode {pad,cut} --nproc <nproc> --outdir <out_dir> --outname <out_name> --pf <primer_field> -d <offset_table> -h, --help -s <seq_files> AlignSets-table command line option --delim <delimiter> --exec <muscle_exec> --failed --outdir <out_dir> --outname <out_name> --reverse -h, --help -p <primer_file> annotationConsensus() (in module presto.Annotation)

AssemblePairs command line option --version -h, --help AssemblePairs-align command line option --1f <head_fields> --2f <tail_fields> --alpha <alpha> --coord {illumina,solexa,sra,454,presto} --delim <delimiter> --failed --fasta --log <log_file> --maxerror <max_error> --maxlen <max_len> --minlen <min_len> --nproc <nproc> --outdir <out_dir> --outname <out_name> --rc {head,tail,both} --scanrev -1 <seq_files_1> -2 <seq_files_2> -h, --help AssemblePairs-join command line option --1f <head_fields> --2f <tail_fields> --coord {illumina,solexa,sra,454,presto} --delim <delimiter> --failed --fasta --gap <gap> --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> --rc {head,tail,both} -1 <seq_files_1> -2 <seq_files_2> -h, --help AssemblePairs-reference command line option --1f <head_fields> --2f <tail_fields> --coord {illumina,solexa,sra,454,presto} --delim <delimiter> --evalue <evalue> --exec <usearch_exec> --failed --fasta --fill --log <log_file> --maxhits <max_hits> --minident <min_ident> --nproc <nproc> --outdir <out_dir> --outname <out_name> --rc {head,tail,both} -1 <seq_files_1> -2 <seq_files_2> -h, --help -r <ref_file>

B

BuildConsensus command line option --act {min,max,sum,set,majority} --bf <barcode_field> --cf <copy_fields> --delim <delimiter> --dep --failed --fasta --freq <min_freq> --log <log_file> --maxdiv <max_diversity> --maxerror <max_error> --maxgap <max_gap> --nproc <nproc> --outdir <out_dir> --outname <out_name> --pf <primer_field> --prcons <primer_freq> --version -h, --help -n <min_count> -q <min_qual> -s <seq_files>

C

calculateDiversity() (in module presto.Sequence) calculateSetError() (in module presto.Sequence) checkSeqEqual() (in module presto.Sequence) ClusterSets command line option --delim <delimiter> --end <seq_end> --exec <usearch_exec> --failed --fasta --id <ident> --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> --start <seq_start> --version -f <barcode_field> -h, --help -k <cluster_field> -s <seq_files> collapseAnnotation() (in module presto.Annotation) CollapseSeq command line option --act {min,max,sum,set} --cf <copy_fields> --delim <delimiter> --failed --fasta --inner --keepmiss --log <log_file> --maxf <max_field> --minf <min_field> --outdir <out_dir> --outname <out_name> --uf <uniq_fields> --version -h, --help -n <max_missing> -s <seq_files> collectSeqQueue() (in module presto.Multiprocessing) CommonHelpFormatter (class in presto.Commandline) compilePrimers() (in module presto.Sequence)

ConvertHeaders command line option --version -h, --help ConvertHeaders-454 command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> ConvertHeaders-genbank command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> ConvertHeaders-generic command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> ConvertHeaders-illumina command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> ConvertHeaders-imgt command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> --simple -h, --help -s <seq_files> ConvertHeaders-sra command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -h, --help -s <seq_files> countSeqFile() (in module presto.IO) countSeqSets() (in module presto.IO)

D

data_count (presto.Multiprocessing.SeqResult attribute)

deleteSeqPositions() (in module presto.Sequence)

E

EstimateError command line option --delim <delimiter> --freq <min_freq> --log <log_file> --maxdiv <max_diversity> --mode {freq,qual} --nproc <nproc> --outdir <out_dir> --outname <out_name> --version -f <set_field> -h, --help -n <min_count> -q <min_qual> -s <seq_files>

F

feedSeqQueue() (in module presto.Multiprocessing) FilterSeq command line option --version -h, --help FilterSeq-length command line option --failed --fasta --inner --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -n <min_length> -s <seq_files> FilterSeq-maskqual command line option --failed --fasta --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -q <min_qual> -s <seq_files> FilterSeq-missing command line option --failed --fasta --inner --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -n <max_missing> -s <seq_files> FilterSeq-quality command line option --failed --fasta --inner --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -q <min_qual> -s <seq_files>

FilterSeq-repeats command line option --failed --fasta --inner --log <log_file> --missing --nproc <nproc> --outdir <out_dir> --outname <out_name> -h, --help -n <max_repeat> -s <seq_files> FilterSeq-trimqual command line option --failed --fasta --log <log_file> --nproc <nproc> --outdir <out_dir> --outname <out_name> --reverse --win <window> -h, --help -q <min_qual> -s <seq_files> findGapPositions() (in module presto.Sequence) flattenAnnotation() (in module presto.Annotation) frequencyConsensus() (in module presto.Sequence)

G

getAAScoreDict() (in module presto.Sequence) getAnnotationValues() (in module presto.Annotation) getCommonArgParser() (in module presto.Commandline) getCoordKey() (in module presto.Annotation)

getDNAScoreDict() (in module presto.Sequence) getFileType() (in module presto.IO) getOutputHandle() (in module presto.IO)

I

indexSeqSets() (in module presto.Sequence)

M

makeUSearchDb() (in module presto.Applications) manageProcesses() (in module presto.Multiprocessing) MaskPrimers command line option --version -h, --help

MaskPrimers-align command line option --barcode --delim <delimiter> --failed --fasta --gap <gap_penalty> --log <log_file> --maxerror <max_error> --maxlen <max_len> --mode {cut,mask,trim,tag} --nproc <nproc> --outdir <out_dir> --outname <out_name> --revpr --skiprc -h, --help -p <primer_file> -s <seq_files> MaskPrimers-score command line option --barcode --delim <delimiter> --failed --fasta --log <log_file> --maxerror <max_error> --mode {cut,mask,trim,tag} --nproc <nproc> --outdir <out_dir> --outname <out_name> --revpr --start <start> -h, --help -p <primer_file> -s <seq_files> mergeAnnotation() (in module presto.Annotation)

P

PairSeq command line option --1f <fields_1> --2f <fields_2> --coord {illumina,solexa,sra,454,presto} --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> --version -1 <seq_files_1> -2 <seq_files_2> -h, --help parseAnnotation() (in module presto.Annotation) parseCommonArgs() (in module presto.Commandline) ParseHeaders command line option --version -h, --help ParseHeaders-add command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -s <seq_files> -u <values> ParseHeaders-collapse command line option --act {min,max,sum,first,last,set,cat} --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -s <seq_files> ParseHeaders-copy command line option --act {min,max,sum,first,last,set,cat} --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -k <names> -s <seq_files> ParseHeaders-delete command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -s <seq_files> ParseHeaders-expand command line option --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> --sep <separator> -f <fields> -h, --help -s <seq_files> ParseHeaders-rename command line option --act {min,max,sum,first,last,set,cat} --delim <delimiter> --failed --fasta --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -k <names> -s <seq_files> ParseHeaders-table command line option --delim <delimiter> --failed --outdir <out_dir> --outname <out_name> -f <fields> -h, --help -s <seq_files>

ParseLog command line option --delim <delimiter> --outdir <out_dir> --outname <out_name> --version -f <fields> -h, --help -l <record_files> presto.Annotation (module) presto.Applications (module) presto.Commandline (module) presto.IO (module) presto.Multiprocessing (module) presto.Sequence (module) printLog() (in module presto.IO) printMessage() (in module presto.IO) printProgress() (in module presto.IO) processSeqQueue() (in module presto.Multiprocessing)

Q

qualityConsensus() (in module presto.Sequence)

R

readPrimerFile() (in module presto.IO) readSeqFile() (in module presto.IO) renameAnnotation() (in module presto.Annotation) reverseComplement() (in module presto.Sequence)

runBlastnAlignment() (in module presto.Applications) runMuscle() (in module presto.Applications) runUBlastAlignment() (in module presto.Applications) runUClust() (in module presto.Applications)

S

scoreAA() (in module presto.Sequence) scoreDNA() (in module presto.Sequence) scoreSeqPair() (in module presto.Sequence) SeqData (class in presto.Multiprocessing) SeqResult (class in presto.Multiprocessing) SplitSeq command line option --version -h, --help SplitSeq-count command line option --fasta --outdir <out_dir> --outname <out_name> -h, --help -n <max_count> -s <seq_files>

SplitSeq-group command line option --delim <delimiter> --fasta --num <threshold> --outdir <out_dir> --outname <out_name> -f <field> -h, --help -s <seq_files> SplitSeq-sample command line option --delim <delimiter> --fasta --outdir <out_dir> --outname <out_name> -f <field> -h, --help -n <max_count> -s <seq_files> -u <values> SplitSeq-samplepair command line option --coord {illumina,solexa,sra,454,presto} --delim <delimiter> --fasta --outdir <out_dir> --outname <out_name> -1 <seq_files_1> -2 <seq_files_2> -f <field> -h, --help -n <max_count> -u <values> SplitSeq-sort command line option --delim <delimiter> --fasta --num --outdir <out_dir> --outname <out_name> -f <field> -h, --help -n <max_count> -s <seq_files> subsetSeqIndex() (in module presto.Sequence) subsetSeqSet() (in module presto.Sequence)

T

translateAmbigDNA() (in module presto.Sequence)

W

weightSeq() (in module presto.Sequence)