Genome Hubs and Browsers

Ensembl Genomes   [http://www.ensemblgenomes.org/]
Gramene Genomes   [http://www.gramene.org/]
NCBI Genomes   [http://www.ncbi.nlm.nih.gov/mapview/]
Phytozome Genomes   [http://www.phytozome.net]
UCSC Genomes   [http://genome.ucsc.edu/cgi-bin/hgGateway]

Gene Prediction Programs

Augustus  [http://augustus.gobics.de/]
FGenesH   [http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind]
GenomeScan   [http://genes.mit.edu/genomescan.html]
GenScan   [http://genes.mit.edu/GENSCAN.html]
SNAP   [http://homepage.mac.com/iankorf/]

Homology Search Programs

BLAST   [http://blast.ncbi.nlm.nih.gov/Blast.cgi]
BLAT   [http://genome.ucsc.edu/cgi-bin/hgBlat?command=start]

Phylogenetic Analysis Program

PHILYP   [http://evolution.genetics.washington.edu/phylip.html]

Sequence Alignment Programs

ClustalW2   [http://www.ebi.ac.uk/Tools/clustalw2/index.html]
MUMmer   [http://mummer.sourceforge.net/]

Sequence Annotation Program

Apollo   [http://www.dhgp.org/current/index.html]

Other Softwares

GBrowse   [http://gmod.org/wiki/GBrowse]
Maker Web Annotation Service   [http://derringer.genetics.utah.edu/cgi-bin/MWAS/maker.cgi]
TARGeT   [http://target.iplantcollaborative.org]