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"planemo upload for repository https://github.com/smirarab/ASTRAL commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty" |
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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 |
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| diff -r 000000000000 -r 66ebc4b19d6c astral.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/astral.xml Wed Apr 13 15:03:31 2022 +0000 |
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| b'@@ -0,0 +1,130 @@\n+<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">\n+ <requirements>\n+ <requirement type="package" version="5.7.8">astral-tree</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[ \n+ astral -i $input1 -t ${branch_annotation_level_selector} -o ./output.tre -c $lambda 2> $log_output\n+ &&\n+ mv ./output.tre $output\n+ #if $branch_annotation_level_selector == "16" or $branch_annotation_level_selector == "32"\n+ &&\n+ mv freqQuad.csv $branch_annotations\n+ #end if;\n+ ]]></command>\n+ <inputs>\n+ <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />\n+ <param name="branch_annotation_level_selector" type="select" label="How much annotations should be added to each branch: 0, 1, or 2.">\n+ <option value="3">3 (default): only the posterior probability for the main resolution.</option>\n+ <option value="0">0: no annotations.</option>\n+ <option value="1">1: only the quartet support for the main resolution.</option>\n+ <option value="2">2: full annotation.</option>\n+ <option value="4">4: three alternative posterior probabilities.</option>\n+ <option value="8">8: three alternative quartet scores.</option>\n+ <option value="16">16: for file export of branch annotations to freqQuad.csv (see below).</option>\n+ <option value="32">32: for file export of branch annotations to freqQuad.csv (see below).</option>\n+ <option value="10">10: p-values of a polytomy null hypothesis test. (default: 3)</option>\n+ </param>\n+ <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\n+ branch lengths and posterior probabilities. Default: 0.5" multiple="false"/>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="newick" label="Output tree file"/>\n+ <data name="log_output" format="txt" label="Astral log."/>\n+ <data name="branch_annotations" format="tabular" label="Branch annotations file.">\n+ <filter>branch_annotation_level_selector == \'16\' or branch_annotation_level_selector == \'32\'</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="song_mammals.424.gene.tre"/>\n+ <param name="branch_annotation_level_selector" value="16" />\n+ <param name="lambda" value="2" />\n+ <output name="output" file="song_mammals.tre" ftype="newick"/>\n+ <output name="log_output">\n+ <assert_contents>\n+ <has_line line="Number of taxa: 37 (37 species)" />\n+ <has_line line="gradient0: 1933" />\n+ <has_line line="Number of Clusters after addition by distance: 1933" />\n+ <has_line line="Final quartet score is: 25526915" />\n+ </assert_contents>\n+ </output>\n+ <output name="branch_annotations" file="freqQuad.csv" ftype="tabular"/>\n+ </test>\n+ <test>\n+ <param name="input1" value="song_primates.424.gene.tre"/>\n+ <param name="branch_annotation_level_selector" value="0" />\n+ <param name="lambda" value="2" />\n+ <output name="output" file="song_primates.tre" ftype="newick"/>\n+ <output name="log_output">\n+ <assert_contents>\n+ <has_line line="Number of taxa: 14 (14 species)" />\n+ <has_line line="gradient0: 339" />\n+ <has_line line="Number of Clusters after addition by distance: 339" />\n+ <has_line line="Final quartet score is: 389734" />\n+ </assert_conten'..b'v outputs, you can use -t 16 and -t 32.\n+ .csv output has the following format.\n+ The output file is always called freqQuad.csv and is written to the same directory as the input file (sorry for the ugliness!)\n+ The file is tab-delimited.\n+ 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.\n+ 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.\n+ 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.\n+ 5th column: number of gene trees that match the the topology in this line.\n+ 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.\n+ 6th column: This is the total number of gene trees that had any useful information about this branch.\n+ If you have no missing data, this should equal the total number of gene trees.\n+ 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.\n+ 4th column is likely you are interested in and it depends on whether you used -t 16 or -t 32.\n+ -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.\n+ -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.\n+\n+Prior hyper-parameter\n+ Our calculations of the local posterior probabilities and branch lengths use a Yule prior model for the branch lengths of the species tree. \n+ 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. \n+ Using -c option one can adjust the hyper-parameter for the prior. \n+ For example, you might want to estimate lambda from the data after one run and plug the estimate prior in a subsequent run. \n+ We have not yet fully explored the impact of lambda on the posterior. \n+ For branch lengths, lambda acts as a pseudocount and can have a substantial impact on the estimated branch length for very long branches. \n+ More specifically, if there is no, or very little discordance around a branch, \n+ the MAP lengths of the branch (which is what we report) is almost fully determined by the prior.\n+\n+ Note that setting lambda to 0 results in reporting ML estimates of the branch lengths instead of MAP. \n+ However, for branches with no discordance, we cannot compute a branch lengths. \n+ For these, we currently arbitrarily set ML to 10 coalescent units (we might change this in future versions).\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="bibtex">\n+@misc{githubASTRAL,\n+ author = {LastTODO, FirstTODO},\n+ year = {TODO},\n+ title = {ASTRAL},\n+ publisher = {GitHub},\n+ journal = {GitHub repository},\n+ url = {https://github.com/smirarab/ASTRAL},\n+}</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 66ebc4b19d6c test-data/README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README Wed Apr 13 15:03:31 2022 +0000 |
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| @@ -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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| diff -r 000000000000 -r 66ebc4b19d6c test-data/bs-files --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bs-files Wed Apr 13 15:03:31 2022 +0000 |
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| diff -r 000000000000 -r 66ebc4b19d6c test-data/freqQuad.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/freqQuad.csv Wed Apr 13 15:03:31 2022 +0000 |
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| b'@@ -0,0 +1,102 @@\n+N0\tt1\t{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}\t1.0\t423.0\t424.0\n+N0\tt2\t{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}\t0.0\t0.0\t424.0\n+N0\tt3\t{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}\t0.0\t1.0\t424.0\n+N1\tt1\t{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}\t1.0\t421.28125\t424.0\n+N1\tt2\t{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}\t0.0\t1.75\t424.0\n+N1\tt3\t{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}\t0.0\t0.96875\t424.0\n+N2\tt1\t{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}\t1.0\t362.2352941176471\t424.0\n+N2\tt2\t{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}\t0.0\t23.88235294117647\t424.0\n+N2\tt3\t{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}\t0.0\t37.88235294117647\t424.0\n+N3\tt1\t{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}\t1.0\t411.34375\t424.0\n+N3\tt2\t{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, '..b'set, Orangutan, Human, Chimpanzee, Gorilla, Macaque, Galagos, Mouse_Lemur, Tarsier}|{Microbat, Megabat, Horse, Dolphin, Cow, Alpaca, Pig, Dog, Cat, Shrew, Hedgehog}\t0.0\t12.360549943883278\t424.0\n+N30\tt3\t{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}\t0.0\t14.031425364758695\t424.0\n+N31\tt1\t{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}\t1.0\t365.6483957219252\t424.0\n+N31\tt2\t{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}\t0.0\t23.886363636363637\t424.0\n+N31\tt3\t{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}\t0.0\t34.46524064171123\t424.0\n+N32\tt1\t{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}\t1.0\t415.10357142857146\t424.0\n+N32\tt2\t{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}\t0.0\t2.7928571428571427\t424.0\n+N32\tt3\t{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}\t0.0\t6.103571428571429\t424.0\n+N33\tt1\t{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}\t1.0\t312.7878787878788\t424.0\n+N33\tt2\t{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}\t0.0\t59.151515151515156\t424.0\n+N33\tt3\t{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}\t0.0\t52.06060606060606\t424.0\n' |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/freqQuadVisualization.R --- /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]); |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/out.log --- /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 |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/out_primates.log --- /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 |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/song_mammals.424.gene.tre --- /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 |
| b |
| b'@@ -0,0 +1,424 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|
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/song_mammals.424genes.bs-trees.zip |
| b |
| Binary file test-data/song_mammals.424genes.bs-trees.zip has changed |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/song_mammals.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/song_mammals.tre Wed Apr 13 15:03:31 2022 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +(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)N34:0.0)N35; |
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/song_primates.424.gene.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/song_primates.424.gene.tre Wed Apr 13 15:03:31 2022 +0000 |
| b |
| b'@@ -0,0 +1,424 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|
| b |
| diff -r 000000000000 -r 66ebc4b19d6c test-data/song_primates.tre --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/song_primates.tre Wed Apr 13 15:03:31 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(Marmoset,((Tarsier,((Galago,Mouse_Lemur),((Horse,Sloth),(Tree_Shrew,(Rat,Rabbit))))),(Macaque,(Orangutan,((Human,Chimpanzee),Gorilla)))):0.0); |