cmgc Ancestral Library

If you use these results in your work, please cite: Hanson-Smith and Johnson, PLoS Comp. Bio., 2016

Overview | Alignments | Sites | Trees | Ancestors | Mutations

ID Alignment

Sequence Alignment Method

Alignments computed by different methods can disagree about which sites are homologous. These differences can, potentially, impact the topology and branch lengths on the maximum likelihood phylogeny.

 		Model

Markov Model

Each model specifies a different substitution pattern between amino acids. These differences can, potentially, lead to different inferences of the best tree topology and branch lengths.

 		log(L)

log(Likelihood)

The log of the likelihood, i.e. the probability of observing all the data in the sequence alignment, given the evolutionary model, the best tree topology, and optimized branch lengths on that tree.

 		Relative
Prob.

Relative Probability

The relatively probability of the phylogeny inferred by this alignment and model, compared to the best phylogenies from other models with this same alignment. The relative probability is computed based on the log(likelihood).

 		Alpha

Alpha

The alpha parameter describes the scale of the distribution of branch lengths. A high value for alpha generally indicates long branches.

 		∑ B.L.

Sum of Branch Lengths

The sum of all branch lengths on the phylogeny.

 		Download

Download

You can download the tree as a Newick-formatted string, viewable by external programs such as FigTree.

 		Statistical
Support

Statistical Support

One or more methods were used to estimate the support for each branch in the phylogeny.

1. The Approximate Likelihood Ratio Test (aLRT)

Anisimova and Gascuel
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
Systematic Biology (2006) 55 (4): 539-552
DOI: 10.1080/10635150600755453

2. The Approximate Likelihood Ratio (aLR), computed from aLRTs. INTERPRETATION: An aLR value of X on branch B indicates that the existence of B is X times more likely than the next-best phylogenetic hypothesis in which B does not exist.

 		Ancestors
0. msaprobs PROTCATLG -258778.74 0.33 1.000 981.73 newick aLRT | aLR view
1. msaprobs PROTCATWAG -258976.12 0.31 1.000 700.11 newick aLRT | aLR view
2. msaprobs PROTCATJTT -258784.23 0.32 1.000 827.84 newick aLRT | aLR view
3. msaprobs PROTGAMMALG -262348.59 0.00 0.562 981.73 newick aLRT | aLR view
4. msaprobs PROTGAMMAWAG -262329.74 0.00 0.639 703.25 newick aLRT | aLR view
5. msaprobs PROTGAMMAJTT -261906.09 0.04 0.603 835.42 newick aLRT | aLR view
6. muscle PROTCATLG -256716.02 0.32 1.000 411.55 newick aLRT | aLR view
7. muscle PROTCATWAG -257327.22 0.27 1.000 313.81 newick aLRT | aLR view
8. muscle PROTCATJTT -256496.34 0.33 1.000 345.99 newick aLRT | aLR view
9. muscle PROTGAMMALG -260564.62 0.00 0.777 416.90 newick aLRT | aLR view
10. muscle PROTGAMMAWAG -260184.41 0.03 0.791 315.24 newick aLRT | aLR view
11. muscle PROTGAMMAJTT -259946.23 0.05 0.717 349.76 newick aLRT | aLR view

Structural Differences Between Trees

The values in this table express symmmetric distance between trees inferred from different combinations of methods and models. The IDs correspond to the row IDs in the table at top. Symmetric distance is computed as the sum of branch splits found in one tree, but not the other tree. For more information, see the DendroPy function 'symmetric_difference'.

ID 0 1 2 3 4 5 6 7 8 9 10 11
0 0.00 22.00 50.00 50.00 44.00 86.00 116.00 106.00 136.00 140.00 134.00 140.00
1 480.00 0.00 44.00 62.00 46.00 82.00 112.00 102.00 132.00 134.00 126.00 132.00
2 488.00 276.00 0.00 62.00 72.00 78.00 114.00 104.00 128.00 138.00 128.00 120.00
3 404.00 448.00 480.00 0.00 52.00 68.00 124.00 112.00 144.00 142.00 134.00 136.00
4 456.00 476.00 482.00 394.00 0.00 50.00 136.00 120.00 154.00 158.00 142.00 150.00
5 486.00 494.00 484.00 486.00 354.00 0.00 150.00 138.00 138.00 172.00 154.00 140.00
6 522.00 534.00 536.00 538.00 536.00 526.00 0.00 40.00 70.00 74.00 60.00 76.00
7 494.00 532.00 526.00 536.00 548.00 522.00 424.00 0.00 80.00 86.00 68.00 78.00
8 520.00 498.00 506.00 526.00 528.00 538.00 436.00 454.00 0.00 116.00 72.00 50.00
9 532.00 528.00 534.00 542.00 510.00 510.00 500.00 496.00 514.00 0.00 74.00 90.00
10 514.00 510.00 512.00 508.00 510.00 530.00 478.00 418.00 342.00 532.00 0.00 58.00
11 532.00 552.00 540.00 540.00 518.00 546.00 470.00 462.00 484.00 502.00 486.00 0.00

Branch Length Differences Between Trees

The values in this table express the Euclidean distance between trees inferred from different combinations of methods and model. The IDs correspond to the row IDs in the table at top. Euclidean distance is the sum of absolute differences in branch lengths for equivalent splits between two trees, with a value of 0.0 for the branch length of a missing split. This is equivalent to the "branch length distance" proposed by Felsenstein (2004). For more information, see the DendroPy function 'euclidean_distance'.

ID 0 1 2 3 4 5 6 7 8 9 10 11
0 0.00 57.88 67.47 61.02 58.32 69.47 60.53 60.90 61.07 61.92 61.37 62.22
1 57.88 0.00 47.39 56.18 43.44 56.49 43.15 41.29 42.41 45.00 41.47 43.07
2 67.47 47.39 0.00 67.63 55.63 59.54 53.81 52.45 53.62 52.53 52.48 53.95
3 61.02 56.18 67.63 0.00 53.92 68.09 61.58 61.66 61.73 62.57 61.38 61.71
4 58.32 43.44 55.63 53.92 0.00 45.29 43.65 42.22 43.25 45.00 42.67 42.56
5 69.47 56.49 59.54 68.09 45.29 0.00 55.48 54.31 54.92 53.74 54.68 54.77
6 60.53 43.15 53.81 61.58 43.65 55.48 0.00 23.95 24.99 31.72 24.90 26.75
7 60.90 41.29 52.45 61.66 42.22 54.31 23.95 0.00 21.23 28.64 18.94 22.74
8 61.07 42.41 53.62 61.73 43.25 54.92 24.99 21.23 0.00 30.15 20.55 24.75
9 61.92 45.00 52.53 62.57 45.00 53.74 31.72 28.64 30.15 0.00 29.24 29.94
10 61.37 41.47 52.48 61.38 42.67 54.68 24.90 18.94 20.55 29.24 0.00 23.56
11 62.22 43.07 53.95 61.71 42.56 54.77 26.75 22.74 24.75 29.94 23.56 0.00

Generated by PhyloBot at 16:11, November 21st 2018
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