MAVID

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.

MAVID
Developer(s)Nicolas Bray (UC Berkeley), Lior Pachter (UC Berkeley)
Stable release
2.0.4
Operating systemUNIX, Linux, Mac
TypeBioinformatics tool
LicenceOpen source
WebsiteMAVID 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

This program accepts sequences in FASTA format.

The output format includes: FASTA format, Clustal, PHYLIP.

gollark: Those are fairly C-like with the main difference being better memory management and some level of object orientation.
gollark: What languages are you meaning specifically? There are many not-particularly-C-like ones.
gollark: I think making a less efficient Python program (with intensive mathy things done via numpy etc. which use bindings to C) makes a lot more sense than having a possibly-faster C program which takes several times longer to write, in most cases.
gollark: It's a poor performance decision (although you can just use pypy, which doesn't have that), sure.
gollark: Although all the tooling and CPUs are optimized for the C model, so good luck changing anything ever.

References
  1. Dewey, Colin N. (2007), "Aligning Multiple Whole Genomes with Mercator and MAVID", in Bergman, Nicholas H. (ed.), Comparative Genomics, Methods in Molecular Biology, 395, Humana Press, pp. 221–235, doi:10.1007/978-1-59745-514-5_14, ISBN 978-1-58829-693-1, PMID 17993677
  2. 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.


This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.