Parallel Implementation and Performance of FastDNAml - A Program for Maximum Likelihood Phylogenetic Inference

This paper describes the parallel implementation of fastDNAml, a program for the maximum likelihood inference of phylogenetic trees from DNA sequence data. Mathematical means of inferring phylogenetic trees have been made possible by the wealth of DNA data now available. Maximum likelihood analysis of phylogenetic trees is extremely computationally intensive. Availability of computer resources is a key factor limiting use of such analyses. fastDNAml is implemented in serial, PVM, and MPI versions, and may be modified to use other message passing libraries in the future. We have developed a viewer for comparing phylogenies. We tested the scaling behavior of fastDNAml on an IBM RS/6000 SP up to 64 processors. The parallel version of fastDNAml is one of very few computational phylogenetics codes that scale well. fastDNAml is available for download as source code or compiled for Linux or AIX.

[1]  F. Brinkman,et al.  Phylogenetic analysis. , 1998, Methods of biochemical analysis.

[2]  Ananth Grama,et al.  Analyzing the Error Bounds of Multipole-Based Treecodes , 1998, Proceedings of the IEEE/ACM SC98 Conference.

[3]  Anil K. Kesarwani,et al.  Genome Informatics , 2019, Encyclopedia of Bioinformatics and Computational Biology.

[4]  Michael R. Fellows,et al.  Two Strikes Against Perfect Phylogeny , 1992, ICALP.

[5]  Yves Van de Peer,et al.  The European Small Subunit Ribosomal RNA database , 2000, Nucleic Acids Res..

[6]  Tandy J. Warnow,et al.  Designing fast converging phylogenetic methods , 2001, ISMB.

[7]  J. Hein,et al.  A tree reconstruction method that is economical in the number of pairwise comparisons used. , 1989, Molecular biology and evolution.

[8]  Ross A. Overbeek,et al.  The RDP (Ribosomal Database Project) , 1997, Nucleic Acids Res..

[9]  Tin Wee Tan,et al.  Maximum Likelihood Analysis Of Phylogenetic Data , 1998 .

[10]  Joaquín Dopazo,et al.  Parallel Implementation of DNAml Program on Message-Passing Architectures , 1998, Parallel Comput..

[11]  G. Olsen.  Phylogenetic analysis using ribosomal RNA. , 1988, Methods in enzymology.

[12]  Mark J. Clement,et al.  Parallel Phylogenetic Inference , 2000, ACM/IEEE SC 2000 Conference (SC'00).

[13]  David A. Bader,et al.  High-Performance Algorithm Engineering for Gene-Order Phylogenies , .

[14]  Joseph Felsenstein,et al.  The number of evolutionary trees , 1978 .

[15]  D. Lipman,et al.  National Center for Biotechnology Information , 2019, Springer Reference Medizin.

[16]  B L Maidak,et al.  The RDP-II (Ribosomal Database Project) , 2001, Nucleic Acids Res..

[17]  Hideo Matsuda,et al.  fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood , 1994, Comput. Appl. Biosci..

[18]  Breakpoint Phylogenies. , 1997, Genome informatics. Workshop on Genome Informatics.

[19]  A. Lapedes,et al.  Timing the ancestor of the HIV-1 pandemic strains. , 2000, Science.

[20]  G. Olsen,et al.  Majority-Rule Consensus of Phylogenetic Trees Obtained by Maximum-Likelihood Analysis , 1997 .