Parallel implementation of DNAml program on message-passing architectures

Parallel Computing

Volumn 24, Issue 5-6, 1998, Pages 701-716

  Ceron, C ^a   Dopazo, J ^b   Zapata, E L ^a   Carazo, J M ^a,c   Trelles, O ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

^b Tecnologias Diagnostico y la Invest   (Spain)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

DNAml program; Parallel computers; Phylogenetic trees; Run time analysis

Indexed keywords

COMPUTER ARCHITECTURE; COMPUTER SOFTWARE; NATURAL SCIENCES COMPUTING; PARALLEL ALGORITHMS;

MESSAGE PASSING COMPUTER ARCHITECTURE; PARALLEL VIRTUAL MACHINES (PVM);

PARALLEL PROCESSING SYSTEMS;

EID: 0032099099     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0167-8191(98)00002-7     Document Type: Article

References (12)

1. Argonne National Laboratory, Early experiences with the IBM SP1 and the High Performance Switch, (Internal Report ANL-93/41, 1993).
2. R. Butler, E. Lusk, User's guide to the P4 programming system, Argonne National Laboratory technical report TM-ANL-92/17, 1992.
3. L.L. Cavalli-Sforza, A.W.F. Edwards, Phylogenetic analysis: models and estimation procedures, Am. J. Hum. Genet. 19 (1967) 233-257.
4. J. Felsenstein, Maximum likelihood estimation of evolutionary trees from continuous characters, Soc. Hum. Genet. 25 (1973) 471-492.
5. J. Felsenstein, Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters, Syst. Zool. 22 (1973) 240-249.
6. J. Felsenstein, Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates, Evolution 35 (1981) 1229-1242.
7. J. Felsenstein, Phylogenies from molecular sequences: inference and reliability, Annu. Rev. Genet. 22 (1988) 521-565.
8. M. Gribskov, J. Devereux, Sequence Analysis Primer, UWBC Biotechnical Resource Series, 1991.
9. G.J. Olsen, H. Matsuda, R. Hagstrom, R. Oberbeek, fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood, CABIOS 10 (1994) 41-48.
10. V.S. Sunderman, PVM: A framework for parallel distributed computing, Concurrency Pract. Experience 2 (1990) 4315-4339.
11. O. Trelles, E.L. Zapata, J.M. Carazo, Mapping strategies for sequential sequence comparison algorithms on LAN-based message passing architectures, Lecture Notes in Computer Science, Vol. 796, 1994a; HPCN.94, Srpinger-Verlag, Berlin, 197-202.
12. O. Trelles, E.L. Zapata, J.M. Carazo, On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures, CABIOS 10 (1994) 5509-5511.