1.UCSC Genome Browser
http://genome.ucsc.edu/
2.ENSEMBL Genome Browser
http://www.ensembl.org/index.html
3.NCBI Map Viewer
http://www.ncbi.nlm.nih.gov/projects/mapview
4.GBrowse
http://gmod.org/wiki/GBrowse
5.NCBI Genome WorkBench
http://www.ncbi.nlm.nih.gov/projects/gbench/
6.IGB
JBrowse
7.IGV Integrative Genomics Viewer
http://www.broadinstitute.org/igv/
8 Seqmonkhttp://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/
SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are:
Web-Based Synteny Browsers
GBrowse_syn http://gmod.org/wiki/GBrowse_syn
SynView http://eupathdb.org/apps/SynView
SynBrowse http://www.synbrowse.org
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