• 1. Blast 2 Sequences
• This tool produces the alignment of two given sequences using BLAST engine for local alignment.

• 2. BLAST: Basic Local Alignment Search Tool
• NCBI. The "BLAST page" offers a number of different BLAST sequence alignment tools for DNA, RNA or proteins. Use "blastn" for nucleotide BLAST

• 3. ClustalW2
• EBI. Perform alignments of multiple DNA or protein sequences.

• 4. Codon Usage Database
• Kazusa. Find the frequency of codon usage in various organisms.

• 5. GenBank
• GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

• 6. Genomes FASTA - Genomes Similarity Search
• EMBL. Use the FASTA ("Fast All) algorithm to run a nucleotide sequence similarity search

• 7. NCBI Entrez Nucleotide
• NCBI. Search for nucleotide sequences from GenBank, RefSeq and PDB. Retrieves curated and archival (non-curated) sequences from a number of sources. Also allows users to submit nucleotide records.

• 8. NCBI Reference Sequence (RefSeq)
• NCBI. Collection of curated non-redundant reference mRNA sequences within GenBank

• 9. ParAlign
• CMBN Bioinformatics Group and Sencel Bioinformatics. Rapid and sensitive sequence similarity searches powered by parallel computing technology.

• 10. SSEARCH
• DDBJ. Perform a Smith-Waserman alignment search on DNA or protein sequences

• 11. The EMBL Nucleotide Sequence Database
• EBI. Europe's main sequence database. Search for nucleotide sequences or submit them.