FastME 


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FastME is a fast phylogeny reconstruction program based on the minimum evolution method. Among distance methods, FastME has shown better topological accuracy than Neighbor Joining, BIONJ, WEIGHBOR and FITCH, in all evolutionary conditions we have tested, including large range deviations from molecular clock and substitution rates. When the number of taxa is high, its superiority over NJ, BIONJ and WEIGHBOR becomes important, while FITCH remains close to FastME but becomes hard to use due to its slowness. FastME is very fast, even faster than NJ, and can easily be applied to very large data sets (> 1000 taxa).( http://gohelle.cirad.fr/galaxy/root )