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FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and recollection. FastTree is open-source software -- you can download the code below.
FastTree is more on the mark than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally in use accustomed to for large alignments.
To account for the benefit of the varying proportions of evolution beyond sites, FastTree uses a single gauge for each locate the "CAT" approximation. To quickly guess the reliability of each split in the tree, FastTree computes local supporter values with the Shimodaira-Hasegawa test these are the at any rate as PhyML 3's "SH-like local supports".
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Each line must be less than 5, characters. More precisely, after optimizing the tree with a fixed rate for each site the CAT model , FastTree will rescale the tree to optimize the Gamma20 likelihood. The support values are the minimum of SH-like and approximate likelihood ratio test supports. For viewing larger trees, I use Archaeopteryx. If you do not have a multiple sequence alignment, we recommend using MUSCLE to create one and gblocks to "trim" it remove low-confidence parts of the alignment, such as positions that contain many gaps.
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However, this will be corrected in the next stage. Freely available at MBE. The support values are the minimum of SH-like and approximate likelihood ratio test supports. Also, the fine-grained nature of the parallelization of the ML code limits the speedup.
For nucleotide sequences, FastTree uses the Jukes-Cantor distance
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