alignReport             Report on alignment
callGenotypes           Make genotype calls
callGenotypes.default   Default internal methods for 'callGenotypes'
combineMlgtResults      Combine two or more mlgtResult objects
createKnownAlleleList   Create 'variantMap' object from allele
                        alignment
dumpVariantMap.mlgtResult
                        Dump variants as fasta
dumpVariants            Print sequence to file
errorCorrect            Alignment error correction
genotypeCall            Results from 'callGenotypes'
getSubSeqsTable         Align and trim sequences for marker/sample pair
getTopBlastHits         Return top blast hits
inspectBlastResults     Plot BLAST statisitics for one marker
mlgt                    Get variants for all markers/samples
mlgt-package            mlgt: Multi-locus geno-typing
mlgtDesign              An S4 class that holds information about an
                        mlgt analysis.
mlgtResult              An S4 class to hold results from 'mlgt'
my.mlgt.Result          An example 'mlgtResult' object.
plotGenotypeEvidence    Plot genotyping evidence
prepareMlgtRun          Prepare to run mlgt
printBlastResultGraphs
                        Plot BLAST statistics for several markers to
                        file
variantMap              An S4 class to hold all unique variants
                        found/known for a marker.
writeGenotypeCallsToFile
                        Write genotype calls to file
