7ca00d20d2c5c137d78f47d364b4d5be09acfb15
dschmelt
Thu Mar 25 17:03:26 2021 -0700
Stashing 2 tools and documenting others for refs #27278
diff --git src/hg/htdocs/util.html src/hg/htdocs/util.html
index 33e4857..79dc196 100755
--- src/hg/htdocs/util.html
+++ src/hg/htdocs/util.html
@@ -1,44 +1,68 @@
-
+
-UCSC Genome Browser Utilities
+Other Tools from the UCSC Genome Browser
-The following tools and utilities created by the UCSC Genome Browser Group are available for
-public use:
+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:
-
- Batch Coordinate Conversion (liftOver) -
- converts genome coordinates and genome annotation files between assemblies. The current version
- supports both forward and reverse conversions, as well as conversions between selected
- species.
+ 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 the phylogenetic tree specification given. Offers several configuration options for branch
- lengths, normalized lengths, branch labels, legend etc.
+ 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