File:Maximum Likelihood-Tree-of-C.cinnamoneus.svg

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Molecular Phylogenetic analysis of Cortinarius cinnamoneus by the Maximum Likelihood method
The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura 3-parameter model [1]. The tree with the highest log likelihood (-1442.8567) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches (the bootstrap test was performed with 1000 replicates). A user-specified Minimum Evolution-tree was used as an initial tree in the heuristic search. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.1184)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved only 29 nucleotide sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 591 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2]. Type-sequences are in bold print. Incorrect identifications are marked with '**'. All C. cinnamoneus-sequences are reddish brown, correct ones are dark reddish brown, the incorrect pale reddish brown.

1. Tamura K. (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution 9:678-687.

2. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.

The following sequences are taken from the [NCBI Nucleotide-Genbank https://www.ncbi.nlm.nih.gov/nuccore/]:

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Author Thkgk
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I, the copyright holder of this work, hereby publish it under the following license:
Creative Commons CC-Zero This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication.
The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.

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Date/TimeThumbnailDimensionsUserComment
current22:16, 6 March 2016Thumbnail for version as of 22:16, 6 March 2016744 × 766 (872 KB)Thkgk (talk | contribs)A last try.
20:27, 6 March 2016Thumbnail for version as of 20:27, 6 March 2016729 × 943 (57 KB)Thkgk (talk | contribs)Tree hopefully corrected.
20:17, 6 March 2016Thumbnail for version as of 20:17, 6 March 2016766 × 744 (50 KB)Thkgk (talk | contribs){{Information |Description= '''Molecular Phylogenetic analysis of ''Cortinarius cinnamoneus'' by the Maximum Likelihood method'''<br/> The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura 3-parameter model [1...

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