PAINT: Leishmania Sexual Reproductive Strategies As Resolved Through Compuational Methods Designed for Aneuploid Genomes

Jahangheer S. Shaik, Deborah E. Dobson, David L. Sacks and Stephen M. Beverley

The following utilities are present in PAINT suite

findAlleles- Finds alleles at genomic positions at specified intervals.
listAlleles - Translates allele file into alleles as indicated by frequency and coverage thresholds.
findSNPsSomy- Finds SNPs based on the chromosomal somies.
findAllelesSNPpositions- Finds composition of all the samples at the selected markers.
findAlleleFreqsSNPpositions- Finds allele frequencies of the samples at the selected markers.
Divide the merged allele into individual chromosomal files.
Divide the merged allele frequency files into individual chromosomal files.
getParentAllelFrequencies- Find allele frequencies of the alleles inherited from both the parental lines.
findReadDepth- Find the coverage values at genomic positions as specified by the interval.
divideReadDepthFile- Divide the coverage file into individual chromosome files.
ConcatenatedPloidyMatrix- Find the chromosomal somies of all the samples in a directory.
FindCommonSpecificReadsWithSynteny- Find reads that are common to two species maintaining synteny and those that are specific to each species.
FindCommonSpecificReads- Find reads that are common to two species and those that are specific to each species.