Genomics Analysis
| Name | Description | Sequence Type* | Link |
|---|---|---|---|
| ACT (Artemis Comparison Tool) | Synteny and comparative genomics | Nucleotide | server |
| AVID | Pairwise global alignment with whole genomes | Nucleotide | server |
| BLAT | Alignment of cDNA sequences to a genome. | Nucleotide | |
| GMAP | Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. | Nucleotide | http://research-pub.gene.com/gmap |
| Splign | Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Able to recognize and separate gene duplications. | Nucleotide | http://www.ncbi.nlm.nih.gov/sutils/splign |
| Mauve | Multiple alignment of rearranged genomes (also available inside Geneious) | Nucleotide | download |
| MGA | Multiple Genome Aligner | Nucleotide | download |
| Mulan | Local multiple alignments of genome-length sequences | Nucleotide | server |
| Multiz | Multiple alignment of genomes | Nucleotide | download |
| PLAST-ncRNA | Search for ncRNAs in genomes by partition function local alignment | Nucleotide | server |
| Sequerome | Profiling sequence alignment data with major servers/services | Nucleotide/peptide | server |
| Sequilab | Profiling sequence alignment data from NCBI-BLAST results with major servers/services | Nucleotide/peptide | server |
| Shuffle-LAGAN | Pairwise glocal alignment of completed genome regions | Nucleotide | server |
| SIBsim4 / Sim4 | A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns | Nucleotide | download |
| SLAM | Gene finding, alignment, annotation (human-mouse homology identification) | Nucleotide | server |
Read more about this topic: List Of Sequence Alignment Software
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