Clann: investigating phylogenetic information through supertree analyses

Summary: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. Availability: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. Supplementary information: Clann has been written in the C programming language. Source code is available on request

Building large phylogenetic trees on coarse-grained parallel machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computa- tional requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efï¬ciency tests that show how to maximise efï¬ciency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public li- cence from the system webpage at http://www.cs.nuim.ie/distribute

Clann: investigating phylogenetic information through supertree analyses

Summary: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. Availability: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. Supplementary information: Clann has been written in the C programming language. Source code is available on request

DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood

Motivation: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialised parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood based phylogenetic analysis. Results: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully crossplatform phylogenetic tree building program called DPRml. It uses an already proven maximum likelihood based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a âfreeâ ML supercomputer. Availability: The software (and user manual) is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.may.ie/distributed Contact: [email protected]

Building large phylogenetic trees on coarse-grained parallel machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computa- tional requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efï¬ciency tests that show how to maximise efï¬ciency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public li- cence from the system webpage at http://www.cs.nuim.ie/distribute

DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood

Motivation: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialised parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood based phylogenetic analysis. Results: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully crossplatform phylogenetic tree building program called DPRml. It uses an already proven maximum likelihood based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a âfreeâ ML supercomputer. Availability: The software (and user manual) is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.may.ie/distributed Contact: [email protected]

Building large phylogenetic trees on coarse-grained parallel machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computa- tional requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efï¬ciency tests that show how to maximise efï¬ciency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public li- cence from the system webpage at http://www.cs.nuim.ie/distribute

DPRml: distributed phylogeny reconstruction by maximum likelihood

Motivation: In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximum likelihood. We express a number of concerns about the current set of parallel phylogenetic programs which are currently severely limiting the widespread availability and use of parallel computing in maximum likelihood-based phylogenetic analysis. Results: We have identified the suitability of phylogenetic analysis to large-scale heterogeneous distributed computing. We have completed a distributed and fully cross-platform phylogenetic tree building program called distributed phylogeny reconstruction by maximum likelihood. It uses an already proven maximum likelihood-based tree building algorithm and a popular phylogenetic analysis library for all its likelihood calculations. It offers one of the most extensive sets of DNA substitution models currently available. We are the first, to our knowledge, to report the completion of a distributed phylogenetic tree building program that can achieve near-linear speedup while only using the idle clock cycles of machines. For those in an academic or corporate environment with hundreds of idle desktop machines, we have shown how distributed computing can deliver a âfreeâ ML supercomputer. Availability: The software (and user manual) is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.may.ie/distributed Contact: [email protected]

Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines

Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computational requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efficiency tests that show how to maximise efficiency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.nuim.ie/distributed