Generic

pslStats
Function: Collect statistics from a psl file.
Usage: pslStats [options] psl statsOut
pslCat
Function: Concatenate psl files
Usage: pslCat file(s)
genePredHisto
Function: Get data for generating histograms from a genePred file.
Usage: genePredHisto [options] what genePredFile histoOut
nibSize
Function: Print size of nibs
Usage: nibSize nib1 [...]
samtools dict
Function: Create a sequence dictionary file from a fasta file.
Usage: samtools dict <ref.fasta|ref.fasta.gz>
clstr_sort_by.pl
Function: This script sort clusters in .clstr file by length, size
Usage: Clstr_sort_by.pl input.clstr no > input_sort.clstr
faNoise
Function: Add noise to fasta file
Usage: faNoise inName outName transitionPpt transversionPpt insertPpt deletePpt chimeraPpt
newProg
Function: Make a new C source skeleton.
Usage: newProg progName description words
pslPretty
Function: Convert PSL to human readable output
Usage: pslPretty in.psl target.lst query.lst pretty.out
textHistogram
Function: Make a histogram in ascii
Usage: textHistogram [options] inFile
bedRestrictToPositions
Function: Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file.
Usage: bedRestrictToPositions in.bed restrict.bed out.bed
hgLoadWiggle
Function: Load a wiggle track definition into database
Usage: hgLoadWiggle [options] database track files(s).wig
pslHisto
Function: Collect counts on PSL alignments for making histograms.
Usage: pslHisto [options] what inPsl outHisto
pslToPslx
Function: Convert from psl to pslx format, which includes sequences
Usage: pslToPslx [options] in.psl qSeqSpec tSeqSpec out.pslx
subChar
Function: Substitute one character for another throughout a file.
Usage: subChar oldChar newChar file(s)