Mercurial > repos > padge > astral
changeset 0:66ebc4b19d6c draft default tip
"planemo upload for repository https://github.com/smirarab/ASTRAL commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
| author | padge |
|---|---|
| date | Wed, 13 Apr 2022 15:03:31 +0000 |
| parents | |
| children | |
| files | astral.xml test-data/README test-data/bs-files test-data/freqQuad.csv test-data/freqQuadVisualization.R test-data/out.log test-data/out_primates.log test-data/song_mammals.424.gene.tre test-data/song_mammals.424genes.bs-trees.zip test-data/song_mammals.tre test-data/song_primates.424.gene.tre test-data/song_primates.tre |
| diffstat | 12 files changed, 1650 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/astral.xml Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,130 @@ +<tool id="astral" name="ASTRAL-III. Tool for estimating an unrooted species tree given a set of unrooted gene trees." version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="5.7.8">astral-tree</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + astral -i $input1 -t ${branch_annotation_level_selector} -o ./output.tre -c $lambda 2> $log_output + && + mv ./output.tre $output + #if $branch_annotation_level_selector == "16" or $branch_annotation_level_selector == "32" + && + mv freqQuad.csv $branch_annotations + #end if; + ]]></command> + <inputs> + <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" /> + <param name="branch_annotation_level_selector" type="select" label="How much annotations should be added to each branch: 0, 1, or 2."> + <option value="3">3 (default): only the posterior probability for the main resolution.</option> + <option value="0">0: no annotations.</option> + <option value="1">1: only the quartet support for the main resolution.</option> + <option value="2">2: full annotation.</option> + <option value="4">4: three alternative posterior probabilities.</option> + <option value="8">8: three alternative quartet scores.</option> + <option value="16">16: for file export of branch annotations to freqQuad.csv (see below).</option> + <option value="32">32: for file export of branch annotations to freqQuad.csv (see below).</option> + <option value="10">10: p-values of a polytomy null hypothesis test. (default: 3)</option> + </param> + <param name="lambda" type="float" optional="true" value="0.5" min="0.0" max="10.0" label="lambda" help="lambda parameter for the Yule prior used in the calculations of + branch lengths and posterior probabilities. Default: 0.5" multiple="false"/> + </inputs> + <outputs> + <data name="output" format="newick" label="Output tree file"/> + <data name="log_output" format="txt" label="Astral log."/> + <data name="branch_annotations" format="tabular" label="Branch annotations file."> + <filter>branch_annotation_level_selector == '16' or branch_annotation_level_selector == '32'</filter> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="song_mammals.424.gene.tre"/> + <param name="branch_annotation_level_selector" value="16" /> + <param name="lambda" value="2" /> + <output name="output" file="song_mammals.tre" ftype="newick"/> + <output name="log_output"> + <assert_contents> + <has_line line="Number of taxa: 37 (37 species)" /> + <has_line line="gradient0: 1933" /> + <has_line line="Number of Clusters after addition by distance: 1933" /> + <has_line line="Final quartet score is: 25526915" /> + </assert_contents> + </output> + <output name="branch_annotations" file="freqQuad.csv" ftype="tabular"/> + </test> + <test> + <param name="input1" value="song_primates.424.gene.tre"/> + <param name="branch_annotation_level_selector" value="0" /> + <param name="lambda" value="2" /> + <output name="output" file="song_primates.tre" ftype="newick"/> + <output name="log_output"> + <assert_contents> + <has_line line="Number of taxa: 14 (14 species)" /> + <has_line line="gradient0: 339" /> + <has_line line="Number of Clusters after addition by distance: 339" /> + <has_line line="Final quartet score is: 389734" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Newick annotations + no annotations (-t 0): This turns off calculation and reporting of posterior probabilities and branch lengths. + Quartet support (-t 1): The percentage of quartets in your gene trees that agree with a branch (normalized quartet support) give use a nice way of measuring the amount of gene tree conflict around a branch. Note that the local posterior probabilities are computed based on a transformation of normalized quartet scores (see Figure 2 of this paper). + Alternative quartet topologies (-t 8): Outputs q1, q2, q3; these three values show quartet support (as defined above) for the main topology (LR|SO), first alternative (RS|LO) and second alternative (RO|LS), respectively. + Local posterior (-t 3): is the default where we show local posterior probability for the main topology. + Alternative posteriors (-t 4): The output includes three local posterior probabilities: one for the main topology, and one for each of the two alternatives (RS|LO and RO|LS, in that order). The posterior of the three topologies adds up to 1. This is because of our locality assumption, which basically asserts that we assume the four groups around the branch (L, R, S, and O) are each correct and therefore, there are only three possible alternatives. + Full annotation (-t 2): When you use this option, for each branch you get a lot of different measurements: + q1,q2,q3: these three values show quartet support (as defined in the description of -t 1) for the main topology, the first alternative, and the second alternative, respectively. + f1, f2, f3: these three values show the total number of quartet trees in all the gene trees that support the main topology, the first alternative, and the second alternative, respectively. + pp1, pp2, pp3: these three show the local posterior probabilities (as defined in the description of -t 4) for the main topology, the first alternative, and the second alternative, respectively. + QC: this shows the total number of quartets defined around each branch (this is what our paper calls m). + EN: this is the effective number of genes for the branch. If you don't have any missing data, this would be the number of branches in your tree. When there are missing data, some gene trees might have nothing to say about a branch. Thus, the effective number of genes might be smaller than the total number of genes. + Polytomy test (-t 10): runs an experimental test to see if a null hypothesis that the branch is a polytomy could be rejected. See this paper: doi:10.3390/genes9030132. + +File export of branch annotations + Since it is often hard to know which branch is L and which branch is R, understanding branch annotations is a bit hard for most users. + To help, we have added a feature for outputting some of the branch annotations into a .csv file. + Note that we strongly suggest using DiscoVista to visualize the quartet frequencies. If you find DiscoVista hard to install and use, you can instead use these .csv files. + +To get the .csv outputs, you can use -t 16 and -t 32. + .csv output has the following format. + The output file is always called freqQuad.csv and is written to the same directory as the input file (sorry for the ugliness!) + The file is tab-delimited. + 1st column: a dummy name for the node. Note that each three lines in a row have the same node number. Around each node, we have three possible unrooted toplogies (NNI rearrangements). We show stats for these three rearrangements. + 2nd column: the topology name for which we are giving the scores. Here, t1 is always the main topology (observed in your species tree) and t2 and t3 are the two alternatives. + 3rd column: Gives the actual topology with the format: {A}|{B}#{C}|{D}. This means that the quartet topology being scored is putting groups A and B together on one side, and groups C and D on the other side. Please remember that quartets are unrooted trees. Each of the groups is a comma-separate list of species. + 5th column: number of gene trees that match the the topology in this line. + You will note that this number is not always an integer number. The reason is that in each gene tree, groups A, B, C, and D may not be together. Those gene trees still count as 1 unit, but they can contribute a fraction of that total of 1 to each of the tree topologies. So a gene tree may count as 0.7 for one topology, 0.2 for another, and 0.1 for the third. + 6th column: This is the total number of gene trees that had any useful information about this branch. + If you have no missing data, this should equal the total number of gene trees. + If you have missing data, some genes may be missing one of groups A, B, C, or D entirely. Those genes will be agnostic about this branch. This column gives the number of genes that have at least one species from each of A, B, C, and D. + 4th column is likely you are interested in and it depends on whether you used -t 16 or -t 32. + -t 16: This column is the local posterior for the topology given in this line. Note that the local posterior probability is different from normalized quartet score. See Figure 2 of this paper. + -t 32: This column is simply 5th column divided by 6 column. Thus, it gives the normalized quartet score for that topology. Note that the three lines with the same node name (1st column) will add up to one in their 4th column. + +Prior hyper-parameter + Our calculations of the local posterior probabilities and branch lengths use a Yule prior model for the branch lengths of the species tree. + The speciation rate (in coalescent units) of the Yule process (lambda) is by default set to 0.5, which results in a flat prior for the quartet frequencies in the [1/3,1] range. + Using -c option one can adjust the hyper-parameter for the prior. + For example, you might want to estimate lambda from the data after one run and plug the estimate prior in a subsequent run. + We have not yet fully explored the impact of lambda on the posterior. + For branch lengths, lambda acts as a pseudocount and can have a substantial impact on the estimated branch length for very long branches. + More specifically, if there is no, or very little discordance around a branch, + the MAP lengths of the branch (which is what we report) is almost fully determined by the prior. + + Note that setting lambda to 0 results in reporting ML estimates of the branch lengths instead of MAP. + However, for branches with no discordance, we cannot compute a branch lengths. + For these, we currently arbitrarily set ML to 10 coalescent units (we might change this in future versions). + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubASTRAL, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {ASTRAL}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/smirarab/ASTRAL}, +}</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,17 @@ +**Song et al**: +We include here sample input files based on the [Song et al.](http://www.pnas.org/content/109/37/14942.short) dataset of 37 mammalian species and 442 genes. +We have removed 23 problematic genes (21 mislabeled genes and 2 genes we classified as outliers) and +we have also re-estimated gene trees using RAxML on the alignments that authors of that paper kindly provided to us. +We have also included 200 replicates of bootstrapped gene trees for the gene trees we estimated on the Song et al. dataset. + +**Simulation**: +We have included simulations based on the Song et al. dataset with increases rates of ILS. + +**primates:** +We have also created a reduced version of the Song et al. dataset with 9 primates, tree shrews, and 4 other mammalian taxa. This dataset is provided for testing the exact version. + +**14 taxon simulation:** +Simulated used SimPhy with extreme levels of ILS + +**100-taxon simulations:** +A simulated dataset with 100 taxa and 2500 bootstrap replicate gene trees is also provided for testing large datasets.
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freqQuad.csv Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,102 @@ +N0 t1 {Chicken, Platypus}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}#{Opossum}|{Wallaby} 1.0 423.0 424.0 +N0 t2 {Chicken, Platypus}|{Opossum}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}|{Wallaby} 0.0 0.0 424.0 +N0 t3 {Chicken, Platypus}|{Wallaby}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}|{Opossum} 0.0 1.0 424.0 +N1 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant}#{Sloth}|{Armadillos} 1.0 421.28125 424.0 +N1 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Sloth}#{Lesser_Hedgehog_Tenrec, Hyrax, Elephant}|{Armadillos} 0.0 1.75 424.0 +N1 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Armadillos}#{Lesser_Hedgehog_Tenrec, Hyrax, Elephant}|{Sloth} 0.0 0.96875 424.0 +N2 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Lesser_Hedgehog_Tenrec}#{Hyrax}|{Elephant} 1.0 362.2352941176471 424.0 +N2 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Hyrax}#{Lesser_Hedgehog_Tenrec}|{Elephant} 0.0 23.88235294117647 424.0 +N2 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Elephant}#{Lesser_Hedgehog_Tenrec}|{Hyrax} 0.0 37.88235294117647 424.0 +N3 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Sloth, Armadillos}#{Lesser_Hedgehog_Tenrec}|{Hyrax, Elephant} 1.0 411.34375 424.0 +N3 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Lesser_Hedgehog_Tenrec}#{Hyrax, Elephant}|{Sloth, Armadillos} 0.0 10.5 424.0 +N3 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Platypus, Opossum, Wallaby}|{Hyrax, Elephant}#{Lesser_Hedgehog_Tenrec}|{Sloth, Armadillos} 0.0 2.15625 424.0 +N4 t1 {Chicken, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}#{Lesser_Hedgehog_Tenrec, Hyrax, Elephant}|{Sloth, Armadillos} 0.9969170843605715 173.08333333333337 424.0 +N4 t2 {Chicken, Platypus, Opossum, Wallaby}|{Sloth, Armadillos}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant} 0.0011399905574400286 119.1815476190476 424.0 +N4 t3 {Chicken, Platypus, Opossum, Wallaby}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}|{Sloth, Armadillos} 0.0019429250819880555 131.73511904761904 424.0 +N5 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}#{Shrew}|{Hedgehog} 1.0 322.09401709401715 424.0 +N5 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Shrew}#{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}|{Hedgehog} 0.0 48.58119658119658 424.0 +N5 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Hedgehog}#{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}|{Shrew} 0.0 53.32478632478632 424.0 +N6 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}#{Microbat}|{Megabat} 1.0 365.04081632653055 424.0 +N6 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat}#{Megabat}|{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat} 0.0 24.464285714285708 424.0 +N6 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Megabat}#{Microbat}|{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat} 0.0 34.49489795918368 424.0 +N7 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Dolphin, Cow, Alpaca, Pig, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse}#{Dog}|{Cat} 1.0 409.49999999999994 424.0 +N7 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Dolphin, Cow, Alpaca, Pig, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dog}#{Horse}|{Cat} 0.0 6.999999999999999 424.0 +N7 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Dolphin, Cow, Alpaca, Pig, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Cat}#{Horse}|{Dog} 0.0 7.499999999999999 424.0 +N8 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dolphin, Cow, Alpaca, Pig}#{Horse}|{Dog, Cat} 0.8909088537282197 159.26249999999996 424.0 +N8 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse}#{Dolphin, Cow, Alpaca, Pig}|{Dog, Cat} 0.060742258548328695 134.48749999999995 424.0 +N8 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dog, Cat}#{Horse}|{Dolphin, Cow, Alpaca, Pig} 0.04834888772345145 130.24999999999997 424.0 +N9 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Alpaca, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Pig}#{Dolphin}|{Cow} 1.0 351.9117647058823 424.0 +N9 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Alpaca, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dolphin}#{Cow}|{Pig} 0.0 48.64705882352941 424.0 +N9 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Alpaca, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Cow}#{Dolphin}|{Pig} 0.0 23.44117647058825 424.0 +N10 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Alpaca}#{Dolphin, Cow}|{Pig} 1.0 275.4848484848485 424.0 +N10 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Pig}#{Dolphin, Cow}|{Alpaca} 1.6427695604349443E-39 69.92424242424242 424.0 +N10 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dolphin, Cow}#{Alpaca}|{Pig} 1.8293534510362302E-39 78.5909090909091 424.0 +N11 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse, Dog, Cat}#{Dolphin, Cow, Pig}|{Alpaca} 1.0 417.04444444444425 424.0 +N11 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Alpaca}#{Horse, Dog, Cat}|{Dolphin, Cow, Pig} 0.0 3.622222222222221 424.0 +N11 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dolphin, Cow, Pig}#{Horse, Dog, Cat}|{Alpaca} 0.0 3.333333333333333 424.0 +N12 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat, Megabat}#{Horse, Dog, Cat}|{Dolphin, Cow, Alpaca, Pig} 0.9962028055973422 172.501488095238 424.0 +N12 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse, Dog, Cat}#{Microbat, Megabat}|{Dolphin, Cow, Alpaca, Pig} 0.002455081521237077 132.76785714285717 424.0 +N12 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Dolphin, Cow, Alpaca, Pig}#{Microbat, Megabat}|{Horse, Dog, Cat} 0.0013421128814213152 118.73065476190476 424.0 +N13 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Shrew, Hedgehog}#{Microbat, Megabat}|{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat} 1.0 240.84340659340648 424.0 +N13 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat, Megabat}#{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}|{Shrew, Hedgehog} 1.692724814889432E-22 98.04395604395603 424.0 +N13 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}#{Microbat, Megabat}|{Shrew, Hedgehog} 1.3302890074552276E-22 85.11263736263733 424.0 +N14 t1 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}#{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}|{Shrew, Hedgehog} 1.0 385.5432098765432 424.0 +N14 t2 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Shrew, Hedgehog}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat} 0.0 18.024691358024686 424.0 +N14 t3 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}|{Shrew, Hedgehog} 0.0 20.432098765432098 424.0 +N15 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel}#{Rabbit}|{Pika} 1.0 415.99999999999994 424.0 +N15 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Rabbit}#{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel}|{Pika} 0.0 6.933333333333334 424.0 +N15 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Pika}#{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel}|{Rabbit} 0.0 1.0666666666666667 424.0 +N16 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Kangaroo_Rat}#{Mouse}|{Rat} 1.0 423.1764705882353 424.0 +N16 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse}#{Rat}|{Kangaroo_Rat} 0.0 0.7941176470588235 424.0 +N16 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Rat}#{Mouse}|{Kangaroo_Rat} 0.0 0.029411764705882353 424.0 +N17 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Guinea_Pig}#{Mouse, Rat}|{Kangaroo_Rat} 1.0 271.87878787878776 424.0 +N17 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Kangaroo_Rat}#{Mouse, Rat}|{Guinea_Pig} 2.1412294986455012E-37 89.46969696969697 424.0 +N17 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat}#{Kangaroo_Rat}|{Guinea_Pig} 0.0 62.651515151515156 424.0 +N18 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Squirrel}#{Mouse, Rat, Kangaroo_Rat}|{Guinea_Pig} 0.9998366402030491 180.92708333333334 424.0 +N18 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Guinea_Pig}#{Mouse, Rat, Kangaroo_Rat}|{Squirrel} 7.210424710013263E-5 118.3645833333333 424.0 +N18 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat, Kangaroo_Rat}#{Guinea_Pig}|{Squirrel} 9.125554985097219E-5 124.70833333333333 424.0 +N19 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Rabbit, Pika}#{Mouse, Rat, Kangaroo_Rat, Guinea_Pig}|{Squirrel} 1.0 371.0374999999999 424.0 +N19 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Squirrel}#{Mouse, Rat, Kangaroo_Rat, Guinea_Pig}|{Rabbit, Pika} 0.0 33.12916666666668 424.0 +N19 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig}#{Squirrel}|{Rabbit, Pika} 0.0 19.83333333333334 424.0 +N20 t1 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tree_Shrew}#{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel}|{Rabbit, Pika} 1.0 303.0793103448278 424.0 +N20 t2 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Rabbit, Pika}#{Tree_Shrew}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel} 0.0 52.27241379310346 424.0 +N20 t3 {Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel}#{Tree_Shrew}|{Rabbit, Pika} 1.0290078116511228E-56 68.64827586206897 424.0 +N21 t1 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}#{Tree_Shrew}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika} 0.8976744589514523 165.04206349206345 424.0 +N21 t2 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tree_Shrew}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika} 0.006295997061756193 106.14761904761906 424.0 +N21 t3 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}|{Tree_Shrew} 0.09602954398679156 152.81031746031746 424.0 +N22 t1 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}#{Galagos}|{Mouse_Lemur} 1.0 399.7397959183673 424.0 +N22 t2 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Galagos}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}|{Mouse_Lemur} 0.0 13.943877551020407 424.0 +N22 t3 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Mouse_Lemur}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}|{Galagos} 0.0 10.316326530612244 424.0 +N23 t1 {Chicken, Marmoset, Orangutan, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Gorilla}#{Human}|{Chimpanzee} 1.0 276.11764705882354 424.0 +N23 t2 {Chicken, Marmoset, Orangutan, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Human}#{Chimpanzee}|{Gorilla} 7.0264141303457595E-40 69.82352941176471 424.0 +N23 t3 {Chicken, Marmoset, Orangutan, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Chimpanzee}#{Human}|{Gorilla} 8.008411231131194E-40 78.05882352941177 424.0 +N24 t1 {Chicken, Marmoset, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Orangutan}#{Human, Chimpanzee}|{Gorilla} 1.0 397.60606060606057 424.0 +N24 t2 {Chicken, Marmoset, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Gorilla}#{Orangutan}|{Human, Chimpanzee} 0.0 16.78787878787879 424.0 +N24 t3 {Chicken, Marmoset, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Human, Chimpanzee}#{Orangutan}|{Gorilla} 0.0 9.606060606060607 424.0 +N25 t1 {Chicken, Marmoset, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Macaque}#{Orangutan}|{Human, Chimpanzee, Gorilla} 1.0 403.5520833333333 424.0 +N25 t2 {Chicken, Marmoset, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Orangutan}#{Human, Chimpanzee, Gorilla}|{Macaque} 0.0 9.604166666666668 424.0 +N25 t3 {Chicken, Marmoset, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Human, Chimpanzee, Gorilla}#{Orangutan}|{Macaque} 0.0 10.84375 424.0 +N26 t1 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset}#{Orangutan, Human, Chimpanzee, Gorilla}|{Macaque} 1.0 405.7258064516129 424.0 +N26 t2 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Macaque}#{Marmoset}|{Orangutan, Human, Chimpanzee, Gorilla} 0.0 11.596774193548388 424.0 +N26 t3 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Orangutan, Human, Chimpanzee, Gorilla}#{Marmoset}|{Macaque} 0.0 6.677419354838709 424.0 +N27 t1 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tarsier}#{Marmoset}|{Orangutan, Human, Chimpanzee, Gorilla, Macaque} 1.0 421.33333333333337 424.0 +N27 t2 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset}#{Orangutan, Human, Chimpanzee, Gorilla, Macaque}|{Tarsier} 0.0 0.9666666666666666 424.0 +N27 t3 {Chicken, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Orangutan, Human, Chimpanzee, Gorilla, Macaque}#{Marmoset}|{Tarsier} 0.0 1.7 424.0 +N28 t1 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Galagos, Mouse_Lemur}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque}|{Tarsier} 1.0 277.26190476190476 424.0 +N28 t2 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tarsier}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque}|{Galagos, Mouse_Lemur} 1.7127445543274987E-40 74.41071428571428 424.0 +N28 t3 {Chicken, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque}#{Galagos, Mouse_Lemur}|{Tarsier} 1.6673751925616003E-40 72.32738095238096 424.0 +N29 t1 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}|{Galagos, Mouse_Lemur} 1.0 391.0477678571429 424.0 +N29 t2 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Galagos, Mouse_Lemur}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}|{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika} 0.0 14.777678571428574 424.0 +N29 t3 {Chicken, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Tarsier}#{Galagos, Mouse_Lemur}|{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika} 0.0 18.17455357142857 424.0 +N30 t1 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}|{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika} 1.0 397.6080246913578 424.0 +N30 t2 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog} 0.0 12.360549943883278 424.0 +N30 t3 {Chicken, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}#{Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Rabbit, Pika}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog} 0.0 14.031425364758695 424.0 +N31 t1 {Chicken, Platypus, Opossum, Wallaby}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog} 1.0 365.6483957219252 424.0 +N31 t2 {Chicken, Platypus, Opossum, Wallaby}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos} 0.0 23.886363636363637 424.0 +N31 t3 {Chicken, Platypus, Opossum, Wallaby}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika}#{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos} 0.0 34.46524064171123 424.0 +N32 t1 {Chicken, Platypus}|{Opossum, Wallaby}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos} 1.0 415.10357142857146 424.0 +N32 t2 {Chicken, Platypus}|{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}|{Opossum, Wallaby} 0.0 2.7928571428571427 424.0 +N32 t3 {Chicken, Platypus}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}#{Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}|{Opossum, Wallaby} 0.0 6.103571428571429 424.0 +N33 t1 {Chicken}|{Platypus}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}|{Opossum, Wallaby} 1.0 312.7878787878788 424.0 +N33 t2 {Chicken}|{Opossum, Wallaby}#{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}|{Platypus} 0.0 59.151515151515156 424.0 +N33 t3 {Chicken}|{Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos}#{Platypus}|{Opossum, Wallaby} 0.0 52.06060606060606 424.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freqQuadVisualization.R Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,8 @@ +#!/usr/bin/env Rscript +red='#d53e4f';orange='#1d91c0';blue='#41b6c4';colormap = c(red,orange,blue) +require(reshape2);require(ggplot2); +dirPath = '.'; filePath = paste(dirPath,'/freqQuadCorrected.csv',sep=''); md<-read.csv(filePath,header=F,sep='\t'); md$value = md$V5/md$V6; +a<-length(levels(as.factor(md$V7)))*3.7; b<-4; sizes <- c(a,b); +md$V8<-reorder(md$V8,-md$value) +ggplot(data=md)+aes(x=V8,y=value,fill=V9)+geom_bar(stat='identity',color=1,width=0.8,position='dodge')+theme_bw()+theme(axis.text.x=element_text(angle=90))+scale_fill_manual(values=colormap,name='Topology')+geom_hline(yintercept=1/3,size=0.4,linetype=2)+ylab('relative freq.')+facet_wrap(~V7,scales='free_x')+xlab('') +pdfFile = paste(dirPath,'/relativeFreq.pdf',sep=''); ggsave(pdfFile,width = sizes[1], height= sizes[2]);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.log Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,62 @@ + +================== ASTRAL ===================== + +This is ASTRAL version 5.7.8 +Gene trees are treated as unrooted +424 trees read from test-data/song_mammals.424.gene.tre +index0 +All output trees will be *arbitrarily* rooted at Chicken + +======== Running the main analysis +Number of taxa: 37 (37 species) +Taxa: [Chicken, Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tree_Shrew, Mouse, Rat, Kangaroo_Rat, Guinea_Pig, Squirrel, Tarsier, Rabbit, Pika, Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog, Lesser_Hedgehog_Tenrec, Hyrax, Elephant, Sloth, Armadillos, Platypus, Opossum, Wallaby] +Taxon occupancy: {Rat=424, Tarsier=424, Dolphin=424, Rabbit=424, Macaque=424, Pika=424, Alpaca=424, Shrew=424, Sloth=424, Tree_Shrew=424, Kangaroo_Rat=424, Armadillos=424, Chimpanzee=424, Horse=424, Dog=424, Human=424, Lesser_Hedgehog_Tenrec=424, Microbat=424, Platypus=424, Wallaby=424, Cow=424, Pig=424, Marmoset=424, Megabat=424, Hedgehog=424, Mouse=424, Guinea_Pig=424, Mouse_Lemur=424, Cat=424, Hyrax=424, Elephant=424, Chicken=424, Orangutan=424, Opossum=424, Galagos=424, Squirrel=424, Gorilla=424} +Number of gene trees: 424 +0 trees have missing taxa +Calculating quartet distance matrix (for completion of X) +Species tree distances calculated ... +Building set of clusters (X) from gene trees +------------------------------ +gradient0: 1933 +Number of Clusters after addition by distance: 1933 +calculating extra bipartitions to be added at level 1 ... +Adding to X using resolutions of greedy consensus ... +Limit for sigma of degrees:975 +polytomy size limit : 4 +discarded polytomies: [3, 3, 4, 4] +Threshold 0.0: +Threshold 0.01: +Threshold 0.02: +Threshold 0.05: +Threshold 0.1: +Threshold 0.2: +polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933 +Threshold 0.3333333333333333: +polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933 +polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 1933 +polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 1933 +max k is :0 +Number of Clusters after addition by greedy: 1933 +gradient0 in heuristiic: 1933 +partitions formed in 0.638 secs +Dynamic Programming starting after 0.638 secs +Using tree-based weight calculation. +Using polytree-based weight calculation. +Polytree max score: 28003080 +Polytree building time: 0.191 seconds. +Number of quartet trees in the gene trees: 28003080 +Size of largest cluster: 37 +Greedy score: 24862814 +estimationFactor: 1.1263037241078182 +Sub-optimal score: 25489533 +Total Number of elements weighted: 3372 +Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9115752624354179 +Optimization score: 25526915 +Optimal tree inferred in 1.287 secs. +(Chimpanzee,(Human,(Gorilla,(Orangutan,(Macaque,(Marmoset,(Tarsier,((Galagos,Mouse_Lemur),((Tree_Shrew,((Rabbit,Pika),(Squirrel,(Guinea_Pig,(Kangaroo_Rat,(Mouse,Rat)))))),((((Chicken,Platypus),(Opossum,Wallaby)),((Sloth,Armadillos),(Lesser_Hedgehog_Tenrec,(Hyrax,Elephant)))),((Shrew,Hedgehog),((Microbat,Megabat),((Horse,(Dog,Cat)),(Alpaca,(Pig,(Dolphin,Cow)))))))))))))))); +Final quartet score is: 25526915 +Final normalized quartet score is: 0.9115752624354179 +Extended species tree: +(Chicken,(Platypus,((Opossum,Wallaby)N0'[pp1=1;pp2=0;pp3=0]':4.04422017503953,(((Sloth,Armadillos)N1'[pp1=1;pp2=0;pp3=0]':3.748755962145693,(Lesser_Hedgehog_Tenrec,(Hyrax,Elephant)N2'[pp1=1;pp2=0;pp3=0]':1.4675747778148045)N3'[pp1=1;pp2=0;pp3=0]':2.8408725661075143)N4'[pp1=1;pp2=0;pp3=0]':0.11272139311072937,(((Shrew,Hedgehog)N5'[pp1=1;pp2=0;pp3=0]':0.9911063406548961,((Microbat,Megabat)N6'[pp1=1;pp2=0;pp3=0]':1.5111714492447694,((Horse,(Dog,Cat)N7'[pp1=1;pp2=0;pp3=0]':2.7358873553893504)N8'[pp1=0.89;pp2=0.06;pp3=0.05]':0.05992302074136598,(Alpaca,(Pig,(Dolphin,Cow)N9'[pp1=1;pp2=0;pp3=0]':1.3217644299037643)N10'[pp1=1;pp2=0;pp3=0]':0.6263941421637529)N11'[pp1=1;pp2=0;pp3=0]':3.259811403201244)N12'[pp1=1;pp2=0;pp3=0]':0.11044150209434113)N13'[pp1=1;pp2=0;pp3=0]':0.42171242314482726)N14'[pp1=1;pp2=0;pp3=0]':1.9051712317138048,((Tree_Shrew,((Rabbit,Pika)N15'[pp1=1;pp2=0;pp3=0]':3.168751437685628,(Squirrel,(Guinea_Pig,(Kangaroo_Rat,(Mouse,Rat)N16'[pp1=1;pp2=0;pp3=0]':4.080152184265601)N17'[pp1=1;pp2=0;pp3=0]':0.6030253811559223)N18'[pp1=1;pp2=0;pp3=0]':0.14397458523452245)N19'[pp1=1;pp2=0;pp3=0]':1.61126493088363)N20'[pp1=1;pp2=0;pp3=0]':0.8259790342993206)N21'[pp1=0.9;pp2=0.01;pp3=0.1]':0.08166400531937129,((Galagos,Mouse_Lemur)N22'[pp1=1;pp2=0;pp3=0]':2.3122034886710434,(Tarsier,(Marmoset,(Macaque,(Orangutan,(Gorilla,(Human,Chimpanzee)N23'[pp1=1;pp2=0;pp3=0]':0.6305518601232605)N24'[pp1=1;pp2=0;pp3=0]':2.2394148609781763)N25'[pp1=1;pp2=0;pp3=0]':2.457113083090445)N26'[pp1=1;pp2=0;pp3=0]':2.550229319109434)N27'[pp1=1;pp2=0;pp3=0]':3.756538102587758)N28'[pp1=1;pp2=0;pp3=0]':0.6381142252128742)N29'[pp1=1;pp2=0;pp3=0]':2.0440320320838024)N30'[pp1=1;pp2=0;pp3=0]':2.239479484018153)N31'[pp1=1;pp2=0;pp3=0]':1.5208686854769229)N32'[pp1=1;pp2=0;pp3=0]':3.0967076693654274)N33'[pp1=1;pp2=0;pp3=0]':0.9068831258917384)N34)N35; +Weight calculation took 0.332760708 secs +ASTRAL finished in 1.713 secs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_primates.log Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,57 @@ + +================== ASTRAL ===================== + +This is ASTRAL version 5.7.8 +Gene trees are treated as unrooted +424 trees read from test-data/song_primates.424.gene.tre +index0 +All output trees will be *arbitrarily* rooted at Marmoset + +======== Running the main analysis +Number of taxa: 14 (14 species) +Taxa: [Marmoset, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galago, Mouse_Lemur, Tree_Shrew, Rat, Tarsier, Rabbit, Horse, Sloth] +Taxon occupancy: {Human=424, Rat=424, Tarsier=424, Galago=424, Rabbit=424, Macaque=424, Sloth=424, Marmoset=424, Tree_Shrew=424, Chimpanzee=424, Mouse_Lemur=424, Horse=424, Orangutan=424, Gorilla=424} +Number of gene trees: 424 +0 trees have missing taxa +Calculating quartet distance matrix (for completion of X) +Species tree distances calculated ... +Building set of clusters (X) from gene trees +------------------------------ +gradient0: 339 +Number of Clusters after addition by distance: 339 +calculating extra bipartitions to be added at level 1 ... +Adding to X using resolutions of greedy consensus ... +Limit for sigma of degrees:400 +polytomy size limit : 3 +discarded polytomies: [3] +Threshold 0.0: +Threshold 0.01: +Threshold 0.02: +Threshold 0.05: +Threshold 0.1: +Threshold 0.2: +Threshold 0.3333333333333333: +polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 339 +max k is :0 +Number of Clusters after addition by greedy: 339 +gradient0 in heuristiic: 339 +partitions formed in 0.192 secs +Dynamic Programming starting after 0.192 secs +Using tree-based weight calculation. +Using polytree-based weight calculation. +Polytree max score: 424424 +Polytree building time: 0.052 seconds. +Number of quartet trees in the gene trees: 424424 +Size of largest cluster: 14 +Greedy score: 389226 +estimationFactor: 1.090430752313566 +Sub-optimal score: 389226 +Total Number of elements weighted: 452 +Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.9182656965675834 +Optimization score: 389734 +Optimal tree inferred in 0.319 secs. +(Gorilla,((Human,Chimpanzee),(Orangutan,(Macaque,(Marmoset,(Tarsier,((Galago,Mouse_Lemur),((Horse,Sloth),(Tree_Shrew,(Rat,Rabbit)))))))))); +Final quartet score is: 389734 +Final normalized quartet score is: 0.9182656965675834 +Weight calculation took 0.027776492 secs +ASTRAL finished in 0.438 secs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/song_mammals.424.gene.tre Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,424 @@ +(Chicken:0.131279775345,(((((((Marmoset:0.0204923957271,((Orangutan:0.00584046083478,((Human:0.00233080025572,Chimpanzee:0.00254878680241):0.000769089390244,Gorilla:0.00176992228314):0.00288531375061):0.00467903448512,Macaque:0.00908469530327):0.00734594094106):0.0296837843809,(Galagos:0.0600055740335,Mouse_Lemur:0.0694590103929):0.0196895108756):0.0085007567437,(Tree_Shrew:0.0534460635684,((((Mouse:0.0349199386903,Rat:0.0345660857178):0.0897288064714,Kangaroo_Rat:0.0649361322722):0.00930431451076,(Guinea_Pig:0.0711517239764,Squirrel:0.0481034437826):0.00498901022113):0.00991061551553,(Tarsier:0.217182450829,(Rabbit:0.0631257980439,Pika:0.087313728905):0.0291647109858):0.0339406584933):0.0030207288372):0.00372275015446):0.00872816165234,((((Microbat:0.0696356706177,Megabat:0.0390727680795):0.0086854921458,(Horse:0.0461656721413,((Dolphin:0.0272954336484,Cow:0.0443204506945):0.0116990944027,(Alpaca:0.051306106068,Pig:0.046407562946):0.00563985340054):0.0247170466469):0.00304339918494):0.00358264486119,(Dog:0.0580489915606,Cat:0.0519621580488):0.0244766206527):0.00494622940371,(Shrew:0.0804342808451,Hedgehog:0.139409366682):0.0210030742124):0.0130522958142):0.00809030960191,((Lesser_Hedgehog_Tenrec:0.156305507638,(Hyrax:0.064198126165,Elephant:0.0292820820713):0.00798950914849):0.0213905471889,(Sloth:0.0383674324752,Armadillos:0.0398080414024):0.0192051567243):0.00316664009477):0.054936328385,Platypus:0.599083136441):0.0419332947834,(Opossum:0.0426931845392,Wallaby:0.0489905851887):0.0753994602564):0.131279775345); +(Chicken:0.13184348409,(((Wallaby:0.0403884889125,Opossum:0.0424549058291):0.0623712854935,Platypus:0.106934421683):0.0265468149082,(((Lesser_Hedgehog_Tenrec:0.0763243234611,(Hyrax:0.0439837309698,Elephant:0.0154182537039):0.00814539614046):0.00927252801896,(((((Cow:0.0253768995556,(Dolphin:0.0137381500408,Pig:0.0515071568701):0.00214247375384):0.00369849062439,Alpaca:0.0327041327444):0.0129939134522,((Microbat:0.0488318249748,(Dog:0.0251914464999,Cat:0.019077962803):0.0156030468259):0.00191908404652,Horse:0.031403746682):0.00190573500035):0.000789098343179,(Megabat:0.0306925352959,(Hedgehog:0.0955938274852,Shrew:0.109121497038):0.0170079661056):0.00357223557112):0.00782417078979,(((Pika:0.0525511270699,Rabbit:0.0390937774654):0.0249464279599,(((Rat:0.0415344954862,Mouse:0.0399640478488):0.0965731665767,Guinea_Pig:0.07749120868):0.0148299066203,(Squirrel:0.0502430198655,Kangaroo_Rat:0.0753162798415):0.00416568798231):0.00545532042101):0.00328679821596,(Tree_Shrew:0.0426560599163,((Tarsier:0.0395620026083,((Macaque:0.00608570187988,(Gorilla:0.00224422775399,(Orangutan:0.00178158136896,(Human:0.00113846667515,Chimpanzee:0.000802993594136):0.000483490555002):2.51049141848e-06):0.00347997654954):0.00821095330186,Marmoset:0.0174481410002):0.0135122407118):0.00305192625139,(Mouse_Lemur:0.0161443473009,Galagos:0.0451624040731):0.0145777943743):0.00233717476908):0.00310699260183):0.00188081676512):0.00884283494833):0.00800323823718,(Sloth:0.0286313631651,Armadillos:0.0298203979513):0.00653477704791):0.100297249941):0.13184348409); +(Chicken:0.200683834898,((((((Hyrax:0.116256868083,Elephant:0.0380072794168):0.0136744583945,Lesser_Hedgehog_Tenrec:0.0757357089314):0.0152092268668,(Armadillos:0.0330496450788,Sloth:0.0390897018537):0.0223747307328):0.00255549065834,((((Dog:0.0380707200472,Cat:0.0219888008619):0.0146010837503,((Megabat:0.026849094959,(Shrew:0.0812377176667,Microbat:0.0385531787149):0.0207936007114):0.0074741804449,(Dolphin:0.0235088724544,(Pig:0.0346116329606,(Cow:0.0431980682584,Alpaca:0.0323155644264):0.00294880915206):0.00313415983936):0.00994396974098):0.00246798483566):0.00165823867717,(Horse:0.037894764365,Hedgehog:0.137100615862):0.00546346949291):0.0118186651971,((((Guinea_Pig:0.0495811955458,Kangaroo_Rat:0.0678327630112):0.00709683048706,(Squirrel:0.0377275552318,(Mouse:0.0291923462182,Rat:0.0305524733839):0.116284752903):0.00823842575795):0.00774685443388,(Pika:0.0595468891827,Rabbit:0.0317487035181):0.0375754712606):0.0038912895723,(Tarsier:0.0516873435361,((Marmoset:0.0311370484253,((Orangutan:0.0152083457523,(Gorilla:0.00129651459821,(Human:0.00245267408963,Chimpanzee:0.0030493338097):0.00121090801175):0.00248508181011):0.00382150588066,Macaque:0.0111332008693):0.00577878387711):0.0137031584176,((Galagos:0.0612751243277,Mouse_Lemur:0.0229549694479):0.0047800435683,Tree_Shrew:0.183791419534):0.00190591845589):0.00370001159991):0.0016619546699):0.00626408623059):0.00747947925016):0.0885583652299,(Wallaby:0.0394521811681,Opossum:0.0396475744035):0.106106659053):0.0500235726093,Platypus:0.107980129272):0.200683834898); 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