Logo of narLink to Publisher's site
Nucleic Acids Res. Nov 11, 1993; 21(22): 5264–5272.
PMCID: PMC310646

MUST, a computer package of Management Utilities for Sequences and Trees.

Abstract

The MUST package is a phylogenetically oriented set of programs for data management and display, allowing one to handle both raw data (sequences) and results (trees, number of steps, bootstrap proportions). It is complementary to the main available software for phylogenetic analysis (PHYLIP, PAUP, HENNING86, CLUSTAL) with which it is fully compatible. The first part of MUST consists of the acquisition of new sequences, their storage, modification, and checking of sequence integrity in files of aligned sequences. In order to improve alignment, an editor function for aligned sequences offers numerous options, such as selection of subsets of sequences, display of consensus sequences, and search for similarities over small sequence fragments. For phylogenetic reconstruction, the choice of species and portions of sequences to be analyzed is easy and very rapid, permitting fast testing of numerous combinations of sequences and taxa. The resulting files can be formatted for most programs of tree construction. An interactive tree-display program recovers the output of all these programs. Finally, various modules allow an in-depth analysis of results, such as comparison of distance matrices, variation of bootstrap proportions with respect to various parameters or comparison of the number of steps per position. All presently available complete sequences of 28S rRNA are furnished aligned in the package. MUST therefore allows the management of all the operations required for phylogenetic reconstructions.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.6M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [PMC free article] [PubMed]
  • Sidow A, Bowman BH. Molecular phylogeny. Curr Opin Genet Dev. 1991 Dec;1(4):451–456. [PubMed]
  • Sogin ML. Early evolution and the origin of eukaryotes. Curr Opin Genet Dev. 1991 Dec;1(4):457–463. [PubMed]
  • Adoutte A, Philippe H. The major lines of metazoan evolution: summary of traditional evidence and lessons from ribosomal RNA sequence analysis. EXS. 1993;63:1–30. [PubMed]
  • Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988;22:521–565. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Qu HL, Michot B, Bachellerie JP. Improved methods for structure probing in large RNAs: a rapid 'heterologous' sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5' terminal domain of eukaryotic 28S rRNA. Nucleic Acids Res. 1983 Sep 10;11(17):5903–5920. [PMC free article] [PubMed]
  • Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. [PubMed]
  • Higgins DG, Bleasby AJ, Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. [PubMed]
  • Feng DF, Doolittle RF. Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol. 1990;183:375–387. [PubMed]
  • Hein J. Unified approach to alignment and phylogenies. Methods Enzymol. 1990;183:626–645. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Li WH, Gouy M. Statistical tests of molecular phylogenies. Methods Enzymol. 1990;183:645–659. [PubMed]
  • Gouy M, Li WH. Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi. Mol Biol Evol. 1989 Mar;6(2):109–122. [PubMed]
  • Graur D, Hide WA, Li WH. Is the guinea-pig a rodent? Nature. 1991 Jun 20;351(6328):649–652. [PubMed]
  • Bailey WJ, Hayasaka K, Skinner CG, Kehoe S, Sieu LC, Slightom JL, Goodman M. Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster. Mol Phylogenet Evol. 1992 Jun;1(2):97–135. [PubMed]
  • Hassouna N, Michot B, Bachellerie JP. The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res. 1984 Apr 25;12(8):3563–3583. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...