| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-psltopslx | public | Convert from psl to pslx format, which includes sequences. | 2025-06-28 |
| ucsc-pslpartition | public | Split PSL files into non-overlapping sets. | 2025-06-28 |
| ucsc-pslrecalcmatch | public | Recalculate match, mismatch, repMatch columns in psl file. | 2025-06-28 |
| ucsc-pslpretty | public | Convert PSL to human-readable output. | 2025-06-28 |
| ucsc-positionaltblcheck | public | Check that positional tables are sorted. | 2025-06-28 |
| ucsc-pslmappostchain | public | Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues. | 2025-06-28 |
| ucsc-pslhisto | public | Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc. | 2025-06-28 |
| ucsc-pslsomerecords | public | Extract multiple psl records. | 2025-06-28 |
| ucsc-pslmap | public | Map PSLs alignments to new targets using alignments of the old target to the new target. | 2025-06-28 |
| ucsc-pslliftsubrangeblat | public | Lift PSLs from blat subrange alignments. | 2025-06-28 |
| ucsc-pslrc | public | Reverse-complement psl. | 2025-06-28 |
| ucsc-addcols | public | Sum columns in a text file. | 2025-06-28 |
| ucsc-ameme | public | Find common patterns in DNA. | 2025-06-28 |
| ucsc-bamtopsl | public | Convert a bam file to a psl and optionally also a fasta file that contains the reads. | 2025-06-28 |
| ucsc-avecols | public | Average together columns. | 2025-06-28 |
| ucsc-axtchain | public | Chain together axt alignments. | 2025-06-28 |
| ucsc-autosql | public | Create SQL and C code for permanently storing. | 2025-06-28 |
| ucsc-autodtd | public | Give this a XML document to look at and it will come up with a DTD. | 2025-06-28 |
| ucsc-axtsort | public | Sort axt files. | 2025-06-28 |
| ucsc-axtswap | public | Swap source and query in an axt file. | 2025-06-28 |
| ucsc-axttomaf | public | Convert from axt to maf format. | 2025-06-28 |
| ucsc-autoxml | public | Generate structures code and parser for XML file from DTD-like spec. | 2025-06-28 |
| ucsc-axttopsl | public | Convert axt to psl format. | 2025-06-28 |
| ucsc-chaintoaxt | public | Convert from chain to axt file. | 2025-06-28 |
| ucsc-chainantirepeat | public | Get rid of chains that are primarily the results of repeats and degenerate DNA. | 2025-06-28 |
