Genome Hubs and Browsers

Ensembl Genomes   Kersey, Paul J., et al. "Ensembl Genomes: extending Ensembl across the taxonomic space." Nucleic acids research 38.suppl 1 (2010): D563-D569.
Gramene Genomes   Ware, Doreen, et al. "Gramene: a resource for comparative grass genomics." Nucleic Acids Research 30.1 (2002): 103-105.
NCBI Genomes   Maglott, Donna, et al. "Entrez Gene: gene-centered information at NCBI." Nucleic acids research 33.suppl 1 (2005): D54-D58.
Phytozome Genomes  
Goodstein, David M., et al. "Phytozome: a comparative platform for green plant genomics." Nucleic acids research 40.D1 (2012): D1178-D1186.
UCSC Genomes  
Karolchik, Donna, et al. "The UCSC genome browser database." Nucleic acids research 31.1 (2003): 51-54.

Gene Prediction Programs

Augustus   [2.6.1]
Stanke, Mario, et al. "AUGUSTUS: a web server for gene finding in eukaryotes." Nucleic acids research 32.suppl 2 (2004): W309-W312.
FGenesH   [3.1.1]
Solovyev V, Kosarev P, Seledsov I, Vorobyev D. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 2006,7, Suppl 1: P. 10.1-10.12.
GenomeScan  
Yeh, Ru-Fang, Lee P. Lim, and Christopher B. Burge. "Computational inference of homologous gene structures in the human genome." Genome research 11.5 (2001): 803-816.
GenScan  
Burge, Chris, and Samuel Karlin. "Prediction of complete gene structures in human genomic DNA." Journal of molecular biology 268.1 (1997): 78-94.
SNAP   [2006-07-28]
Korf, Ian. "Gene finding in novel genomes." BMC bioinformatics 5.1 (2004): 59.

Homology Search Programs

BLAST  [2.2.18]
Altschul, Stephen F., et al. "Basic local alignment search tool." Journal of molecular biology 215.3 (1990): 403-410.
BLAT  
Kent, W. James. "BLAT—the BLAST-like alignment tool." Genome research 12.4 (2002): 656-664.

Phylogenetic Analysis Program

PHILYP  [3.69]
Felsenstein, J. "PHYLIP-Phylogeny Inference Package (Version 3.2) Cladistics 5: 164–166." Find this article online (1989).

Sequence Alignment Programs

ClustalW2  
Larkin, Mark A., et al. "Clustal W and Clustal X version 2.0." Bioinformatics 23.21 (2007): 2947-2948.
MUMmer  
Delcher, Arthur L., et al. "Fast algorithms for large-scale genome alignment and comparison." Nucleic acids research 30.11 (2002): 2478-2483.
MUSCLE  [3.8.31]
Edgar, Robert C. "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic acids research 32.5 (2004): 1792-1797.

Sequence Annotation Program

Apollo  [1.14]
Lewis, Suzanna E., et al. "Apollo: a sequence annotation editor." Genome Biol 3.12 (2002): 1-14.

Other Software

GBrowse  
Stein, Lincoln D., et al. "The generic genome browser: a building block for a model organism system database." Genome research 12.10 (2002): 1599-1610.
Maker Web Annotation Service  
Cantarel, Brandi L., et al. "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes." Genome research 18.1 (2008): 188-196.
RepeatMasker  [open-3.3.0]
Smit, Arian FA, Robert Hubley, and P. Green. "RepeatMasker." Published on the web at http://www. repeatmasker. org (1996).
TARGeT  
Han, Yujun, James M. Burnette, and Susan R. Wessler. "TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences." Nucleic acids research 37.11 (2009): e78-e78.
tRNAscan-SE  [1.23]
Lowe, Todd M., and Sean R. Eddy. "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence." Nucleic acids research 25.5 (1997): 0955-964.

Next Generation Sequencing Program

FastQC  [0.11.2]
Andrews, S. "FastQC: A quality control tool for high throughput sequence data." Reference Source (2010).
Fastx-toolkit  [0.0.13]
Gordon, A., and G. J. Hannon. "Fastx-toolkit." FASTQ/A short-reads preprocessing tools (unpublished) http://hannonlab. cshl. edu/fastx_toolkit (2010).
TopHat  [2.0.11]
Trapnell, Cole, Lior Pachter, and Steven L. Salzberg. "TopHat: discovering splice junctions with RNA-Seq." Bioinformatics 25.9 (2009): 1105-1111.
Cufflinks [2.1.1]
Trapnell, Cole, et al. "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation." Nature biotechnology 28.5 (2010): 511-515.
Cuffdiff [2.1.1]
Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RNA-seq." Nature biotechnology 31.1 (2013): 46-53.