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"Improving the
efficiency of SPR moves in Phylogenetic Tree Search Algorithms based on
Maximum-Likelihood."
W. Hordijk and O. Gascuel. Bioinformatics, 21
(24), 4338-4347, 2005.
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ContentHere you can find executables and data sets as used in our Bioinformatics paper. We would like to note, however, that the program is still very much in a development stage, and is not guaranteed to be bug-free, crash-free, or in any other way problem-free. |
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UsageThe SPR algorithm is implemented in PHYML, and uses the same arguments as the original program. By default, the additional SPR parameters (N_RGRFT, N_GLOBL, and MAX_DIST) are set to 10%, 5%, and 5% of the number of taxa in the data set, respectively. However, if a file "params.spr" exists in the current working directory, the program will read the parameter values from this file. They should be given on one (the first) line, separated by one or more spaces, e.g.:30 20 10 which will set the parameter values to N_RGRFT=30, N_GLOBL=20, and MAX_DIST=10, in that order. |
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DownloadThere are two executables available. The first one, spr, uses the SPR algorithm alone. The second one, ph_spr, uses a combination of the original PHYML and new SPR algorithms. The programs were compiled on a linux system. Finally, the seven data sets used in our paper are also available here.Executables: spr and ph_spr Data sets: 101 taxa, 150 taxa, 250 taxa, 132 taxa, 42 taxa, 39 taxa, and 35 taxa. |
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If you use this software, please cite both :W. Hordijk and O. Gascuel, "Improving the efficiency of SPR moves in Phylogenetic Tree Search Algorithms based on Maximum-Likelihood," Bioinformatics, 21 (24), 4338-4347, 2005. downloadS. Guindon and O. Gascuel, "PHYML, a simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood," Systematic Biology, 52(5), 696-704, 2003. PHYML web site (paper, binaries, server, and more) |
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ContactsFor any questions about the algorithm, the options of the program or the source code, you can contact : |
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