Code, data and supplementary material from: Analyzing phylogenetic trees with a tree lattice coordinate system and a graph polynomial
Data files
Mar 14, 2022 version files 18.89 GB
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ABCL1.Rdata
269.76 MB
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ABCL10.Rdata
2.62 GB
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ABCL2.Rdata
529.08 MB
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ABCL3.Rdata
788.02 MB
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ABCL4.Rdata
1.05 GB
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ABCL5.Rdata
1.31 GB
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ABCL6.Rdata
1.57 GB
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ABCL7.Rdata
1.83 GB
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ABCL8.Rdata
2.09 GB
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ABCL9.Rdata
2.35 GB
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ABCSS1.Rdata
94.51 MB
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ABCSS10.Rdata
97.91 MB
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ABCSS2.Rdata
96.02 MB
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ABCSS3.Rdata
96.63 MB
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ABCSS4.Rdata
96.91 MB
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ABCSS5.Rdata
97.14 MB
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ABCSS6.Rdata
97.46 MB
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ABCSS7.Rdata
97.62 MB
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ABCSS8.Rdata
97.78 MB
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ABCSS9.Rdata
97.94 MB
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BDTrees.Rdata
61.95 MB
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explosiveRadiation-tips500.nwk
207.97 MB
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Flu1.Rdata
855 B
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Flu2.Rdata
846 B
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Flu3.Rdata
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Flu4.Rdata
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hivtrees.Rdata
3.86 MB
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Hunt.nwk
32.87 KB
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Hunt.Rdata
832 B
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MSL.Rdata
15.22 KB
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MSLM.Rdata
13.60 KB
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MSSS.Rdata
22.72 KB
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MSTrees.Rdata
595.60 MB
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Nov.Rdata
836 B
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Novitsky.nex
48.54 KB
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RCK_TS.Rdata
554 B
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README.txt
6.96 KB
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ResL1.Rdata
61.58 KB
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ResL10.Rdata
61.65 KB
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ResL2.Rdata
61.66 KB
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ResL3.Rdata
61.66 KB
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ResL4.Rdata
61.68 KB
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ResL5.Rdata
61.64 KB
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ResL6.Rdata
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ResL7.Rdata
61.72 KB
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ResL8.Rdata
61.62 KB
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ResL9.Rdata
61.66 KB
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ResLM1.Rdata
57.58 KB
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ResLM10.Rdata
56.58 KB
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ResLM2.Rdata
57.35 KB
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ResLM3.Rdata
56.98 KB
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ResLM4.Rdata
57.34 KB
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ResLM5.Rdata
57.30 KB
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ResLM6.Rdata
57.06 KB
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ResLM7.Rdata
56.85 KB
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ResLM8.Rdata
56.91 KB
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ResLM9.Rdata
56.60 KB
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ResSS1.Rdata
59.13 KB
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ResSS10.Rdata
58.36 KB
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ResSS2.Rdata
58.84 KB
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ResSS3.Rdata
58.70 KB
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ResSS4.Rdata
58.72 KB
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ResSS5.Rdata
58.62 KB
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ResSS6.Rdata
58.69 KB
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ResSS7.Rdata
58.46 KB
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ResSS8.Rdata
58.33 KB
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ResSS9.Rdata
58.58 KB
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RL_BD.Rdata
393 B
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RL_TS.Rdata
503 B
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RLM_BD.Rdata
418 B
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RLM_TS.Rdata
518 B
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RP_TS.Rdata
461 B
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RSS_BD.Rdata
532 B
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RSS_TS.Rdata
571 B
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Set1.Rdata
39.44 MB
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Set10.Rdata
445.02 MB
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Set2.Rdata
82.87 MB
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Set3.Rdata
126.83 MB
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Set4.Rdata
173.29 MB
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Set5.Rdata
217.68 MB
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Set6.Rdata
263.26 MB
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Set7.Rdata
308.59 MB
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Set8.Rdata
355.31 MB
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Set9.Rdata
398.80 MB
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traitEvolution-tips500.nwk
216.43 MB
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TreeShapes.Rdata
15.25 MB
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TruePars.Rdata
575.73 KB
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who_clade_trees.Rdata
763.36 KB
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Wolf.nwk
59.70 KB
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Wolf.Rdata
837 B
Abstract
This dataset includes code, used and generated data for the experiments in the paper Analyzing Phylogenetic Trees with a Tree Lattice Coordinate System and a Graph Polynomial, and the supplementary material of the paper. The paper introduces representation and comparison methods for rooted unlabelled phylogenetic trees based on a tree lattice that serves as a coordinate system for rooted binary trees with branch lengths and a graph polynomial that fully characterizes tree shapes. The methods provide fast, accurate, likelihood-free, distance-based appraoches to analyzing phylogenetic trees and allow analysis for large trees with more than a thousand taxa.
The dataset has three sections. The first section is the implementation of the introduced methods for phylogenetic tree analysis as an R package, inlcuding the source code and the binary of the package. This packege provides basic functions for tree analysis and can be used or edited for related analysis. The secoond section includes all code for analyses performed in the the paper, and all the data used and generated in the analyses. The third section contains the supplementary material for the paper, which includes supplememntary results and figures. For details, please refer to the paper and the README file.