 | MurkaSoftware for working with median networks and Steiner trees from alignments of biological sequences. |
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Murka Description
Software for working with median networks and Steiner trees from alignments of biological sequences. Murka is a free software for inferring parsimonistic phylogenies (i.e. trees of minimum cost) from alignments of biological sequences. The theory behind this software is a combination of two algorithmic approaches: building median networks (introduced in early 80s in Algebra and later appeared to be very useful in Phylogenetics) and extracting Steiner trees from graphs. The advantage of this combination is almost complete coverage of the minimum cost trees from a source alignment and tolerate performance for many instances hardly to be completely solved by classical methods, particularly those working with topologies. In addition to exact algorithms, heuristic methods are available too. Murka is not the first program in this field. There are at least two publically available and free software packages targeted at working with median networks. It is Fluxus Engineering Network and AWC Spectronet. Murka seems to be the first opensource program coming with no copyright limitations and distributed under LGPL. Murka includes a Steiner problem solver of weak performance, however it is able to solve most of the the medium-size (of 2K-3K edges) SteinLib benchmarks in reasonable time. The input and output file formats are compatible with those used by Fluxus Network. The Steiner solver works with STP files. For visualization of resulting networks we chose the .dot format of GraphViz software. Murka is a command-line software tested under Linux and Windows platforms. Currently two gardware platforms are supported: x86(is-32) and ia-64 (Itanium2).
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