Other Tools from the UCSC Genome Browser
The UCSC Genome Browser team develops and updates the following main tools:
the Genome Browser,
BLAT, In-Silico PCR,
Table Browser, and LiftOver.
We maintain the following less-used tools: Gene Sorter,
Genome Graphs, and
Data Integrator.
These are available from the "Tools" dropdown menu at the top of the site.
We also offer command-line utilities for many file conversions and basic bioinformatics functions.
You can learn more and download these utilities through the
utilities section
of our downloads page.
The following tools and utilities created by the UCSC Genome Browser Group are also available
for public use:
-
UShER (for SARS-CoV-2 only) -
allows placement of SARS-CoV-2 sequences onto existing phylogenetic trees for tracing strains
and transmission events.
-
Gene Interactions -
displays a gene interaction and pathway graph based on data from curated protein-interaction
databases and text mining of PubMed abstracts.
-
-
displays high-quality images of in-situ mouse and frogs with gene mRNA hybridization
probes and transcription factors.
-
DNA Duster -
removes formatting characters and other non-sequence-related characters from an input sequence.
Offers several configuration options for the output format, including translated protein.
-
Protein
Duster - removes formatting characters and other non-sequence-related characters
from an input sequence. Offers several configuration options for the output format.
-
Phylogenetic Tree PNG Maker - creates a PNG image
from phylogenetic tree specification given; several configuration options for branch
lengths, normalized lengths, branch labels, legend, etc.
-
Executable and
Source Code Downloads - executable and source code downloads of the Genome Browser,
Blat and liftOver.
The following tools and utilities created by outside groups may be helpful when working with our
file formats and the genome annotation databases that we provide. References to these tools are
provided for the benefit of our users. We are unable to support the use of externally developed
tools; if you have questions or problems, please contact the developers of the tool directly.
- BEDOPS -
A highly scalable and easily-parallelizable genome analysis toolkit
- bedtools -
A swiss-army knife of tools for a wide-range of genomics analysis tasks
- bwtool -
A command-line utility for bigWig files
- CrossMap -
A program for genome coordinate conversion between different assemblies
- CruzDb -
Python package to load genome annotations from our servers
- libBigWig -
A C library to read bigWig files, without a dependency on our source code
- MakeHub -
Python tool to build assembly hub files for new genomes
- RTracklayer -
R package to import genome annotations from our databases
- trackhub -
Python package to manage files in our trackDb format
- twobitreader - Python package to open
2bit genome sequence files
- ucsc-genomes-download -
Python package to download genome sequences from our servers
- WiggleTools -
C++ Unix command-line tool to work with bigWig files: combine, merge, scale, aggregate and many other operations