These tools are summarized from a forum in Bioinformatics
To see the original information, click the link bellow.
Circos, this software was published in Genome Research. For overview of all the gemones, not the detail information of genes.
Broad's IGV: https://www.broadinstitute.org/igv/ for genome browsing.
Apparently you can talk to it via https, but you can't say anything very complicated: https://www.broadinstitute.org/igv/PortCommands
UCSC Genome Browser https://genome.ucsc.edu/goldenPath/help/customTrack.html
useful link:
https://plindenbaum.blogspot.com/2009/11/java-implementation-of-jan-aerts.html
For desktop level genome visualization the Integrated Genome Browser is a very nice tool.
Annoj with a nice demo here: https://neomorph.salk.edu/epigenome/epigenome.html seems to be a pretty nice web-interface
Artemis and ACT from the Sanger Institute. The former is a genome viewer and annotation tool. The latter is used for comparing genomes.
Genboree, It's essentially a genome browser with personalized databases/wikis, access control, and integration with Galaxy. It can import UCSC tracks and you can add any data that maps to genomic coordinates. It also has a REST API that's fairly new.
Bioperl's Bio::Graphics
GenomeGraphs, an R Bioconductor package. It fetches annotations from Ensembl and plots them as tracks. It's a good way to overlay quantitative data onto genomic features: here is a sample plot.
