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MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences.[1][2] The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. The latest version is 2.0.4.
Developer(s) | Nicolas Bray (UC Berkeley), Lior Pachter (UC Berkeley) |
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Stable release | 2.0.4
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Operating system | UNIX, Linux, Mac |
Type | Bioinformatics tool |
Licence | Open source |
Website | MAVID download |
The program can be used through the MAVID web server or as a standalone program which can be installed with the source code.
Input/Output
editThis program accepts sequences in FASTA format.
The output format includes: FASTA format, Clustal, PHYLIP.
References
edit- ^ Dewey, Colin N. (2007), "Aligning Multiple Whole Genomes with Mercator and MAVID", in Bergman, Nicholas H. (ed.), Comparative Genomics, Methods in Molecular Biology, vol. 395, Humana Press, pp. 221–235, doi:10.1007/978-1-59745-514-5_14, ISBN 978-1-58829-693-1, PMID 17993677221-235&rft.pub=Humana Press&rft.date=2007&rft_id=info:pmid/17993677&rft_id=info:doi/10.1007/978-1-59745-514-5_14&rft.isbn=978-1-58829-693-1&rft.aulast=Dewey&rft.aufirst=Colin N.&rfr_id=info:sid/en.wikipedia.org:MAVID" class="Z3988">
- ^ Bray, Nicolas; Pachter, Lior (2003-07-01). "MAVID multiple alignment server". Nucleic Acids Research. 31 (13): 3525–3526. doi:10.1093/nar/gkg623. ISSN 0305-1048. PMC 169029. PMID 12824358.3525-3526&rft.date=2003-07-01&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169029#id-name=PMC&rft.issn=0305-1048&rft_id=info:pmid/12824358&rft_id=info:doi/10.1093/nar/gkg623&rft.aulast=Bray&rft.aufirst=Nicolas&rft.au=Pachter, Lior&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169029&rfr_id=info:sid/en.wikipedia.org:MAVID" class="Z3988">
- Bray, N.; Pachter, L. (2004), "MAVID: Constrained ancestral alignment of multiple sequences", Genome Research, 14 (4): 693–699, arXiv:q-bio/0311018, doi:10.1101/gr.1960404, PMC 383315, PMID 15060012693-699&rft.date=2004&rft_id=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383315#id-name=PMC&rft_id=info:pmid/15060012&rft_id=info:arxiv/q-bio/0311018&rft_id=info:doi/10.1101/gr.1960404&rft.aulast=Bray&rft.aufirst=N.&rft.au=Pachter, L.&rfr_id=info:sid/en.wikipedia.org:MAVID" class="Z3988">.