diff --git a/tools/drhip/.shed.yml b/tools/drhip/.shed.yml
new file mode 100644
index 00000000000..66aa2355935
--- /dev/null
+++ b/tools/drhip/.shed.yml
@@ -0,0 +1,13 @@
+categories:
+ - Phylogenetics
+ - Sequence Analysis
+description: Data Reduction for HyPhy with Inference Processing. A toolkit for analyzing
+ and summarizing HyPhy evolutionary selection analysis results
+long_description: |
+ DRHIP processes and summarizes evolutionary selection analysis results from HyPhy
+ across multiple methods (BUSTED, FEL, MEME, PRIME, RELAX, Contrast-FEL) and genes.
+ It generates combined CSV files with gene-level and site-specific statistics.
+name: drhip
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip
+homepage_url: https://github.com/veg/DRHIP
diff --git a/tools/drhip/drhip.xml b/tools/drhip/drhip.xml
new file mode 100644
index 00000000000..a2b34ed20f0
--- /dev/null
+++ b/tools/drhip/drhip.xml
@@ -0,0 +1,248 @@
+
+ Data Reduction for HyPhy with Inference Processing
+
+ 0.1.3
+ 0
+ 25.0
+
+
+ drhip
+
+ drhip --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+ relax_files or contrastfel_files
+
+
+ relax_files or contrastfel_files
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@software{drhip2024,
+ author = {Callan, Danielle and Verdonk, Hannah and Kosakovsky Pond, Sergei L},
+ title = {DRHIP: Data Reduction for HyPhy with Inference Processing},
+ year = {2024},
+ url = {https://github.com/veg/DRHIP},
+ version = {0.1.3}
+}
+
+
+
\ No newline at end of file
diff --git a/tools/drhip/test-data/BUSTED/gene1.json b/tools/drhip/test-data/BUSTED/gene1.json
new file mode 100644
index 00000000000..cd0c2da99e3
--- /dev/null
+++ b/tools/drhip/test-data/BUSTED/gene1.json
@@ -0,0 +1,713 @@
+{
+ "Evidence Ratios":{
+ },
+ "Site Log Likelihood":{
+ "unconstrained": [
+[-3.290019315059098, -4.175663627535955, -4.175663627535955, -4.173115241795732, -9.238614141422939, -6.201388047751721, -3.588161705747214, -3.846065275733122, -11.6279127051655, -4.374967447338868, -4.667251719415955, -5.369450552211644, -4.609545779703736, -4.521369648345189, -3.290019315059098, -4.472687242532417, -3.396709886941963, -5.214702609387182, -4.561720576655006, -3.577740971164724, -4.175663627535955, -5.214702609387182, -4.169795185009985, -4.22785259313233, -4.775958986232662, -11.23524464752527, -14.05898845363783, -4.364741485582735, -4.188622564988608, -4.561720576655006, -3.588161705747214, -3.577740971164724, -4.609545779703736, -4.22785259313233, -10.80905338405208, -4.290623032758742, -4.188622564988608, -9.102696648764709, -10.15065862754325, -5.109026588357197, -7.639966748483763, -4.290623032758742, -5.27139973585393, -3.290019315059098, -3.396709886941963, -15.39005248416766, -4.169795185009985, -3.290019315059098, -5.490588024798257, -8.79815567312038, -3.128919286251878, -4.354491537508268, -4.609545779703736, -4.273615502328157, -3.577740971164724, -7.949833968989759, -4.273615502328157, -5.166376479360413, -3.128919286251878, -9.523238743964589, -4.460708940557628, -3.638165346693491, -4.354491537508268, -7.804776345656695, -4.358412699477345, -4.188622564988608, -5.490588024798257, -3.577740971164724, -4.171027191490039, -11.91661958005109, -4.22785259313233, -4.609545779703736, -3.588161705747214, -3.588161705747214, -4.521369648345189, -4.290623032758742, -4.561720576655006, -4.032579906673688, -3.396709886941963, -4.169795185009985, -11.49141288792201, -4.628717534587926, -5.434467285003718, -9.922930097774541, -6.229068584733115, -3.396709886941963, -6.925748094379387, -4.032579906673688, -4.22785259313233, -4.346914805883308, -3.290019315059098, -8.47331136085584, -6.844904286989593, -3.128919286251878, -3.290019315059098, -6.844904286989593, -6.396159179643725, -3.768797718390692, -3.396709886941963, -3.577740971164724]
+ ]
+ },
+ "Synonymous site-posteriors": [
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+ ],
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond",
+ "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
+ "contact":"spond@temple.edu",
+ "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
+ "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+ "settings":{
+ "error-sink":1,
+ "mss":"No",
+ "multiple-hit":"None",
+ "srv":"Yes"
+ },
+ "version":"4.6"
+ },
+ "background":1,
+ "branch attributes":{
+ "0":{
+ "Node3":{
+ "MG94xREV with separate rates for branch sets":0.007049012269592678,
+ "Nucleotide GTR":0.007289662052004695,
+ "Posterior prob omega class": [
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+ [0.06461204144565623],
+ [2.086325080203871e-05]
+ ],
+ "Posterior prob omega class by site": [
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+ ],
+ "unconstrained":0.006866927675951353
+ },
+ "Node4":{
+ "MG94xREV with separate rates for branch sets":0.01560819603098484,
+ "Nucleotide GTR":0.01388744473547059,
+ "Posterior prob omega class": [
+[0],
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+ [0.02998649797196691],
+ [2.77586925402575e-08]
+ ],
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+ ],
+ "Log Likelihood":-535.0231635224093,
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+ "non-synonymous/synonymous rate ratio for *test*": [
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+ "Rate Distributions":{
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+ "Substitution rate from nucleotide C to nucleotide T":2.269319946484975,
+ "Substitution rate from nucleotide G to nucleotide T":0.1391184331291334
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+ "Synonymous site-to-site rates":{
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+ "display order":2,
+ "estimated parameters":45
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+ "input":{
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+ "number of sequences":9,
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+ "69":{
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+ "79":{
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+ "8":{
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+ "80":{
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+ "81":{
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+ "82":{
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+ "83":{
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+ "84":{
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+ "85":{
+ "root":"AAA"
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+ "86":{
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+ "94":{
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+ "95":{
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+ "96":{
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+ "98":{
+ "root":"AAA"
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+ "99":{
+ "root":"AGA"
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+ }
+ },
+ "test results":{
+ "LRT":0,
+ "p-value":0.5
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+ "tested":{
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+ "Node4":"test",
+ "Node7":"test",
+ "PP563828_1_2023_09_04":"background",
+ "PP563831_1_2023_08_29":"background",
+ "PP563832_1_2023_08_28":"background",
+ "PP563838_1_2023_09_30":"background",
+ "PP563839_1_2023_09_29":"background",
+ "PP563845_1_2023_10_22":"background",
+ "PP563880_1_2023_10_05":"background",
+ "PP563884_1_2023_09_24":"background",
+ "PP564823_1_2023_10_06":"background"
+ }
+ },
+ "timers":{
+ "Overall":{
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+ "timer":28
+ },
+ "Preliminary model fitting":{
+ "order":1,
+ "timer":2
+ },
+ "Unconstrained BUSTED model fitting":{
+ "order":2,
+ "timer":25
+ }
+ }
+}
diff --git a/tools/drhip/test-data/BUSTED/gene2.json b/tools/drhip/test-data/BUSTED/gene2.json
new file mode 100644
index 00000000000..08e4eb1c710
--- /dev/null
+++ b/tools/drhip/test-data/BUSTED/gene2.json
@@ -0,0 +1,695 @@
+{
+ "Evidence Ratios":{
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+ "Site Log Likelihood":{
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+ ],
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond",
+ "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
+ "contact":"spond@temple.edu",
+ "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
+ "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
+ "settings":{
+ "error-sink":1,
+ "mss":"No",
+ "multiple-hit":"None",
+ "srv":"Yes"
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+ "version":"4.6"
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+ "tested":{
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+ "PP563839_1_2023_09_29":"background",
+ "PP563845_1_2023_10_22":"background",
+ "PP564823_1_2023_10_06":"background"
+ }
+ },
+ "timers":{
+ "Overall":{
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+ "timer":30
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+ "Preliminary model fitting":{
+ "order":1,
+ "timer":2
+ },
+ "Unconstrained BUSTED model fitting":{
+ "order":2,
+ "timer":26
+ }
+ }
+}
diff --git a/tools/drhip/test-data/CONTRASTFEL/gene2.json b/tools/drhip/test-data/CONTRASTFEL/gene2.json
new file mode 100644
index 00000000000..b235164acf9
--- /dev/null
+++ b/tools/drhip/test-data/CONTRASTFEL/gene2.json
@@ -0,0 +1,816 @@
+{
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+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0]
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+ },
+ "headers": [
+["alpha", "Synonymous substitution rate at a site"],
+ ["beta (background)", "Non-synonymous substitution rate at a site for background branches"],
+ ["beta (Reference)", "Non-synonymous substitution rate at a site for Reference branches"],
+ ["beta (Foreground)", "Non-synonymous substitution rate at a site for Foreground branches"],
+ ["subs (Reference)", "Substitutions mapped to Reference branches"],
+ ["subs (Foreground)", "Substitutions mapped to Foreground branches"],
+ ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: Reference,Foreground"],
+ ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: Reference,Foreground"],
+ ["Permutation p-value", "Label permutation test for significant sites"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"]
+ ]
+ },
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond and Steven Weaver",
+ "citation":"Mol Biol Evol (2021), (38)3 1184–1198",
+ "contact":"spond@temple.edu",
+ "help":"http://www.hyphy.org/methods/other/contrast-fel/",
+ "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles. Version 0.6 adds detailed ancestral state reconstruction",
+ "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported",
+ "settings":{
+ "site-filter":{
+ "site-filter":null,
+ "site-save-filter":null
+ }
+ },
+ "version":"0.6"
+ },
+ "branch attributes":{
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+ "Model fitting":{
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+ "Total time":{
+ "order":0,
+ "timer":5
+ }
+ }
+}
diff --git a/tools/drhip/test-data/FEL/gene1.json b/tools/drhip/test-data/FEL/gene1.json
new file mode 100644
index 00000000000..2aa20d84806
--- /dev/null
+++ b/tools/drhip/test-data/FEL/gene1.json
@@ -0,0 +1,357 @@
+{
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+ },
+ "headers": [
+["alpha", "Synonymous substitution rate at a site"],
+ ["beta", "Non-synonymous substitution rate at a site"],
+ ["alpha=beta", "The rate estimate under the neutral model"],
+ ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
+ ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
+ ]
+ },
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",
+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
+ "contact":"spond@temple.edu",
+ "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis. Version 2.5 adds MH support.\n ",
+ "requirements":"in-frame codon alignment and a phylogenetic tree",
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+}
diff --git a/tools/drhip/test-data/FEL/gene2.json b/tools/drhip/test-data/FEL/gene2.json
new file mode 100644
index 00000000000..afe19316df4
--- /dev/null
+++ b/tools/drhip/test-data/FEL/gene2.json
@@ -0,0 +1,345 @@
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+ ["beta", "Non-synonymous substitution rate at a site"],
+ ["alpha=beta", "The rate estimate under the neutral model"],
+ ["LRT", "Likelihood ratio test statistic for beta = alpha, versus beta &neq; alpha"],
+ ["p-value", "Asymptotic p-value for evidence of selection, i.e. beta &neq; alpha"],
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+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",
+ "contact":"spond@temple.edu",
+ "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis. Version 2.5 adds MH support.\n ",
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+ [0.0132212670023302],
+ [0.02341317633368553],
+ [0.009744994946783913]
+ ],
+ "Log Likelihood":-522.0389997890163,
+ "Rate Distributions":{
+ "non-synonymous/synonymous rate ratio for *background*": [
+[0.2130893675277186, 1]
+ ],
+ "non-synonymous/synonymous rate ratio for *test*": [
+[0.05367140804417245, 1]
+ ]
+ },
+ "display order":1,
+ "estimated parameters":26
+ },
+ "Nucleotide GTR":{
+ "AIC-c":1130.795872905925,
+ "Equilibrium frequencies": [
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+ [0.2033333333333333],
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+ "Log Likelihood":-546.2152441452704,
+ "Rate Distributions":{
+ "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0,
+ "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+ "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+ "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
+ },
+ "display order":0,
+ "estimated parameters":19
+ }
+ },
+ "input":{
+ "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/66/caf0861a1e46548e7f15d9b82a4920/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
+ "number of sequences":7,
+ "number of sites":100,
+ "partition count":1,
+ "trees":{
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+ }
+ },
+ "runtime":"2.5.73",
+ "tested":{
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+ "Node8":"test",
+ "PP563830_1_2023_09_02":"background",
+ "PP563831_1_2023_08_29":"background",
+ "PP563832_1_2023_08_28":"background",
+ "PP563838_1_2023_09_30":"background",
+ "PP563839_1_2023_09_29":"background",
+ "PP563845_1_2023_10_22":"background",
+ "PP564823_1_2023_10_06":"background"
+ }
+ },
+ "timers":{
+ "FEL analysis":{
+ "order":2,
+ "timer":4
+ },
+ "Model fitting":{
+ "order":1,
+ "timer":1
+ },
+ "Total time":{
+ "order":0,
+ "timer":5
+ }
+ }
+}
diff --git a/tools/drhip/test-data/MEME/gene1.json b/tools/drhip/test-data/MEME/gene1.json
new file mode 100644
index 00000000000..241b58eaeef
--- /dev/null
+++ b/tools/drhip/test-data/MEME/gene1.json
@@ -0,0 +1,558 @@
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+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0]
+ ]
+ },
+ "headers": [
+["α", "Synonymous substitution rate at a site"],
+ ["β1", "Non-synonymous substitution rate at a site for the negative/neutral evolution component 1"],
+ ["p1", "Mixture distribution weight allocated to negative/neutral evolution component 1"],
+ ["β+", "Non-synonymous substitution rate at a site for the positive selection component"],
+ ["p+", "Mixture distribution weight allocated to the positive selection component"],
+ ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"],
+ ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"],
+ ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
+ ["MEME LogL", "Site Log-likelihood under the MEME model"],
+ ["FEL LogL", "Site Log-likelihood under the FEL model"],
+ ["FEL α", "Synonymous substitution rate at a site under the FEL model"],
+ ["FEL β", "Non-synonymous substitution rate at a site under the FEL model"]
+ ]
+ },
+ "analysis":{
+ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
+ "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
+ "contact":"spond@temple.edu",
+ "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis. Version 3.0 adds a different format for ancestral state reconstruction, branch-site posterior storage, and site-level heterogeneity testing. \n Version 4 adds support for multiple hits and more than 2 rate classes on omega, as well as site-level imputation option.\n Version 4.1 fixes bugs with EBF computation for > 2 more rates and MH reporting.\n ",
+ "requirements":"in-frame codon alignment and a phylogenetic tree",
+ "settings":{
+ "Imputed States":0,
+ "fit-mode":0,
+ "multihit":"None",
+ "rates":2,
+ "site-filter":{
+ "site-filter":null,
+ "site-save-filter":null
+ }
+ },
+ "version":"4.1"
+ },
+ "branch attributes":{
+ "0":{
+ "Node3":{
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+ "Nucleotide GTR":0.007289662052004695,
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+ ]
+ },
+ "Node4":{
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+ "Nucleotide GTR":0.01388744473547059,
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+ "Node7":{
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diff --git a/tools/drhip/test-data/MEME/gene2.json b/tools/drhip/test-data/MEME/gene2.json
new file mode 100644
index 00000000000..833548dc345
--- /dev/null
+++ b/tools/drhip/test-data/MEME/gene2.json
@@ -0,0 +1,542 @@
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+ [39.49915549621659, 0, 1, 0.812775496266388, 0, 0, 0.6666666666666666, 0, 0, -5.096248925128101, -5.095585856681431, 0.9993371513345987, 38.16080804119245],
+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0],
+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0],
+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0]
+ ]
+ },
+ "headers": [
+["α", "Synonymous substitution rate at a site"],
+ ["β1", "Non-synonymous substitution rate at a site for the negative/neutral evolution component 1"],
+ ["p1", "Mixture distribution weight allocated to negative/neutral evolution component 1"],
+ ["β+", "Non-synonymous substitution rate at a site for the positive selection component"],
+ ["p+", "Mixture distribution weight allocated to the positive selection component"],
+ ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"],
+ ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"],
+ ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
+ ["MEME LogL", "Site Log-likelihood under the MEME model"],
+ ["FEL LogL", "Site Log-likelihood under the FEL model"],
+ ["FEL α", "Synonymous substitution rate at a site under the FEL model"],
+ ["FEL β", "Non-synonymous substitution rate at a site under the FEL model"]
+ ]
+ },
+ "analysis":{
+ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
+ "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
+ "contact":"spond@temple.edu",
+ "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis. Version 3.0 adds a different format for ancestral state reconstruction, branch-site posterior storage, and site-level heterogeneity testing. \n Version 4 adds support for multiple hits and more than 2 rate classes on omega, as well as site-level imputation option.\n Version 4.1 fixes bugs with EBF computation for > 2 more rates and MH reporting.\n ",
+ "requirements":"in-frame codon alignment and a phylogenetic tree",
+ "settings":{
+ "Imputed States":0,
+ "fit-mode":0,
+ "multihit":"None",
+ "rates":2,
+ "site-filter":{
+ "site-filter":null,
+ "site-save-filter":null
+ }
+ },
+ "version":"4.1"
+ },
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+ ]
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+ "Nucleotide GTR":1e-06,
+ "original name":"PP563830_1_2023_09_02"
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+ "Nucleotide GTR":1e-06,
+ "original name":"PP563839_1_2023_09_29"
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+ "Nucleotide GTR":0.04195089101557686,
+ "original name":"PP564823_1_2023_10_06"
+ }
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+ "attributes":{
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+ "attribute type":"branch length",
+ "display order":1
+ },
+ "Nucleotide GTR":{
+ "attribute type":"branch length",
+ "display order":0
+ },
+ "Posterior prob omega class by site":{
+ "attribute type":"branch annotations",
+ "display order":-1
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+ "original name":{
+ "attribute type":"node label",
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+ }
+ }
+ },
+ "data partitions":{
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+ ],
+ "name":"meme.filter.default"
+ }
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+ "fits":{
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+ "Log Likelihood":-522.0389908680933,
+ "Rate Distributions":{
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+ "non-synonymous/synonymous rate ratio for *test*": [
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+ "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0,
+ "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+ "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+ "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
+ },
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+ "estimated parameters":19
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+ "input":{
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+}
diff --git a/tools/drhip/test-data/PRIME/gene1.json b/tools/drhip/test-data/PRIME/gene1.json
new file mode 100644
index 00000000000..0a3b53b0904
--- /dev/null
+++ b/tools/drhip/test-data/PRIME/gene1.json
@@ -0,0 +1,807 @@
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+ [4.914564863748615, 3.825517957831295e-05, 4.942314687200942, 0.000439307469113938, 0.1276192570232928, 0, 1, -5.981342388813351, -5.981396500108888, 0.9999999999935192, 1, 0.700797868595009, 1, -5.981355107032072, 6.466094596027407, 1, -5.981355281298811, 13.7225092906117, 1, -5.98135445349318, 13.7225092906117, 1, -5.981353743952748, 13.7225092906117, 1, -5.981354974254561],
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+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+ [4.914564863748615, 3.825517957831295e-05, 4.942314687200942, 0.000439307469113938, 0.1276192570232928, 0, 1, -5.981342388813351, -5.981396500108888, 0.9999999999935192, 1, 0.700797868595009, 1, -5.981355107032072, 6.466094596027407, 1, -5.981355281298811, 13.7225092906117, 1, -5.98135445349318, 13.7225092906117, 1, -5.981353743952748, 13.7225092906117, 1, -5.981354974254561],
+ [7.1268309052325, 0.0008467082930323556, 7.161605714085979, 0.007631547187472146, 0.1850664077680016, 0, 1, -5.265925031101748, -5.267110890177635, 0.9999999854407621, 1, 0.8643253215095575, 1, -5.265962739484887, 2.031993017396854, 1, -5.265972083906938, 14.46698601821335, 1, -5.265988045249418, 14.57600442508006, 1, -5.265957445794986, 14.87789987563041, 1, -5.265961254444006],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0]
+ ]
+ },
+ "headers": [
+["α", "Synonymous substitution rate at a site"],
+ ["β", "Property independent non-synonymous rate a site"],
+ ["FEL α", "Synonymous substitution rate at a site (FEL model)"],
+ ["FEL β", "Log of property independent non-synonymous rate a site"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
+ ["# subs", "The number of amino-acid substitutions that occurred at this site"],
+ ["# aa", "The number of unique amino-acids occurring at that site"],
+ ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
+ ["FEL LogL", "Site Log-likelihood under the FEL model"],
+ ["p-value", "Omnibus q-value (any property is important)"],
+ ["q-value", "Importance for Factor I bipolar"],
+ ["λ1", "p-value for non-zero effect of Factor I bipolar"],
+ ["p1", "Log likelihood when there is no effect of Factor I bipolar"],
+ ["LogL1", "Importance for Factor II secondary structure"],
+ ["λ2", "p-value for non-zero effect of Factor II secondary structure"],
+ ["p2", "Log likelihood when there is no effect of Factor II secondary structure"],
+ ["LogL2", "Importance for Factor III volume"],
+ ["λ3", "p-value for non-zero effect of Factor III volume"],
+ ["p3", "Log likelihood when there is no effect of Factor III volume"],
+ ["LogL3", "Importance for Factor IV composition"],
+ ["λ4", "p-value for non-zero effect of Factor IV composition"],
+ ["p4", "Log likelihood when there is no effect of Factor IV composition"],
+ ["LogL4", "Importance for Factor V charge"],
+ ["λ5", "p-value for non-zero effect of Factor V charge"],
+ ["p5", "Log likelihood when there is no effect of Factor V charge"],
+ ["LogL5", "0"]
+ ],
+ "substitutions":{
+ "0":{
+ "0":null,
+ "1":null,
+ "10":null,
+ "11":null,
+ "12":null,
+ "13":null,
+ "14":null,
+ "15":null,
+ "16":null,
+ "17":null,
+ "18":null,
+ "19":null,
+ "2":null,
+ "20":null,
+ "21":null,
+ "22":null,
+ "23":null,
+ "24":null,
+ "25":{
+ "PP564823_1_2023_10_06":"GGT",
+ "root":"GTT"
+ },
+ "26":{
+ "Node3":"TCA",
+ "Node4":"CCA",
+ "PP564823_1_2023_10_06":"TCA",
+ "root":"CCA"
+ },
+ "27":null,
+ "28":null,
+ "29":null,
+ "3":null,
+ "30":null,
+ "31":null,
+ "32":null,
+ "33":null,
+ "34":{
+ "PP563831_1_2023_08_29":"GAA",
+ "root":"AAA"
+ },
+ "35":null,
+ "36":null,
+ "37":{
+ "Node7":"CTT",
+ "root":"CTC"
+ },
+ "38":{
+ "PP563884_1_2023_09_24":"TTA",
+ "root":"TCA"
+ },
+ "39":null,
+ "4":{
+ "Node4":"CGA",
+ "PP564823_1_2023_10_06":"CGG",
+ "root":"CGG"
+ },
+ "40":{
+ "Node4":"CAA",
+ "root":"CAG"
+ },
+ "41":null,
+ "42":null,
+ "43":null,
+ "44":null,
+ "45":{
+ "PP563880_1_2023_10_05":"CTA",
+ "PP564823_1_2023_10_06":"ATG",
+ "root":"CTG"
+ },
+ "46":null,
+ "47":null,
+ "48":null,
+ "49":{
+ "Node3":"TTC",
+ "root":"TTT"
+ },
+ "5":{
+ "PP564823_1_2023_10_06":"AAG",
+ "root":"AAA"
+ },
+ "50":null,
+ "51":null,
+ "52":null,
+ "53":null,
+ "54":null,
+ "55":{
+ "Node4":"TTT",
+ "root":"TTC"
+ },
+ "56":null,
+ "57":null,
+ "58":null,
+ "59":{
+ "Node3":"CCC",
+ "root":"CCT"
+ },
+ "6":null,
+ "60":null,
+ "61":null,
+ "62":null,
+ "63":{
+ "Node4":"GGA",
+ "root":"GGG"
+ },
+ "64":null,
+ "65":null,
+ "66":null,
+ "67":null,
+ "68":null,
+ "69":{
+ "Node4":"GGC",
+ "PP564823_1_2023_10_06":"AGC",
+ "root":"GGT"
+ },
+ "7":null,
+ "70":null,
+ "71":null,
+ "72":null,
+ "73":null,
+ "74":null,
+ "75":null,
+ "76":null,
+ "77":null,
+ "78":null,
+ "79":null,
+ "8":{
+ "PP564823_1_2023_10_06":"GGT",
+ "root":"GCT"
+ },
+ "80":{
+ "PP563838_1_2023_09_30":"CTG",
+ "PP564823_1_2023_10_06":"TTA",
+ "root":"CTA"
+ },
+ "81":null,
+ "82":null,
+ "83":{
+ "PP563832_1_2023_08_28":"TTT",
+ "root":"TTC"
+ },
+ "84":{
+ "PP564823_1_2023_10_06":"AAA",
+ "root":"AAG"
+ },
+ "85":null,
+ "86":{
+ "PP564823_1_2023_10_06":"GAG",
+ "root":"GAA"
+ },
+ "87":null,
+ "88":null,
+ "89":null,
+ "9":null,
+ "90":null,
+ "91":{
+ "Node4":"TTG",
+ "PP564823_1_2023_10_06":"CTG",
+ "root":"CTG"
+ },
+ "92":{
+ "PP564823_1_2023_10_06":"AAC",
+ "root":"AAT"
+ },
+ "93":null,
+ "94":null,
+ "95":{
+ "PP564823_1_2023_10_06":"AAC",
+ "root":"AAT"
+ },
+ "96":{
+ "PP564823_1_2023_10_06":"AGG",
+ "root":"AGA"
+ },
+ "97":null,
+ "98":null,
+ "99":null
+ }
+ }
+ },
+ "analysis":{
+ "authors":"Sergei L. Kosakovsky Pond",
+ "citation":"TBD",
+ "contact":"spond@temple.edu",
+ "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
+ "requirements":"in-frame codon alignment and a phylogenetic tree",
+ "residue_properties":"Atchley",
+ "version":"0.2.0"
+ },
+ "branch attributes":{
+ "0":{
+ "Node3":{
+ "Global MG94xREV":0.007049643511684335,
+ "Nucleotide GTR":0.007289662052004695
+ },
+ "Node4":{
+ "Global MG94xREV":0.01561082867520729,
+ "Nucleotide GTR":0.01388744473547059
+ },
+ "Node7":{
+ "Global MG94xREV":0.006613667342454805,
+ "Nucleotide GTR":0.006185828741026453
+ },
+ "PP563828_1_2023_09_04":{
+ "Global MG94xREV":0,
+ "Nucleotide GTR":1e-06,
+ "original name":"PP563828_1_2023_09_04"
+ },
+ "PP563831_1_2023_08_29":{
+ "Global MG94xREV":0.003311403263977385,
+ "Nucleotide GTR":0.0033386370737857,
+ "original name":"PP563831_1_2023_08_29"
+ },
+ "PP563832_1_2023_08_28":{
+ "Global MG94xREV":0.003310210799301318,
+ "Nucleotide GTR":0.003341256955363836,
+ "original name":"PP563832_1_2023_08_28"
+ },
+ "PP563838_1_2023_09_30":{
+ "Global MG94xREV":0.003319901980605924,
+ "Nucleotide GTR":0.003338636346485376,
+ "original name":"PP563838_1_2023_09_30"
+ },
+ "PP563839_1_2023_09_29":{
+ "Global MG94xREV":0,
+ "Nucleotide GTR":1e-06,
+ "original name":"PP563839_1_2023_09_29"
+ },
+ "PP563845_1_2023_10_22":{
+ "Global MG94xREV":0.00588335347636994,
+ "Nucleotide GTR":0.007154900994762849,
+ "original name":"PP563845_1_2023_10_22"
+ },
+ "PP563880_1_2023_10_05":{
+ "Global MG94xREV":0.003316207961324058,
+ "Nucleotide GTR":0.003342118030716714,
+ "original name":"PP563880_1_2023_10_05"
+ },
+ "PP563884_1_2023_09_24":{
+ "Global MG94xREV":0.00331431000421138,
+ "Nucleotide GTR":0.003341256955567041,
+ "original name":"PP563884_1_2023_09_24"
+ },
+ "PP564823_1_2023_10_06":{
+ "Global MG94xREV":0.0443955944090025,
+ "Nucleotide GTR":0.04196108121510467,
+ "original name":"PP564823_1_2023_10_06"
+ }
+ },
+ "attributes":{
+ "Global MG94xREV":{
+ "attribute type":"branch length",
+ "display order":1
+ },
+ "Nucleotide GTR":{
+ "attribute type":"branch length",
+ "display order":0
+ },
+ "original name":{
+ "attribute type":"node label",
+ "display order":-1
+ }
+ }
+ },
+ "data partitions":{
+ "0":{
+ "coverage": [
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
+ ],
+ "name":"prime.filter.default"
+ }
+ },
+ "fits":{
+ "Global MG94xREV":{
+ "AIC-c":1127.910824156187,
+ "Equilibrium frequencies": [
+[0.04024763514913952],
+ [0.01922996663172304],
+ [0.03420070900547616],
+ [0.014368896284083],
+ [0.03368306905822573],
+ [0.01609347460151461],
+ [0.02862242313127222],
+ [0.01202526618107644],
+ [0.03424262136543949],
+ [0.01636082378008254],
+ [0.02909790661151763],
+ [0.01222503317454278],
+ [0.04878002735358049],
+ [0.02330666869812213],
+ [0.04145116886040549],
+ [0.01741506429336918],
+ [0.01835841860430346],
+ [0.008771491191067078],
+ [0.0156001944004883],
+ [0.006554179193076294],
+ [0.01536407988586604],
+ [0.007340822446772941],
+ [0.01305573416590236],
+ [0.0054851637757677],
+ [0.0156193121609741],
+ [0.007462770186447074],
+ [0.01327261957388795],
+ [0.005576284808737427],
+ [0.02225035479396483],
+ [0.01063102412468302],
+ [0.01890739435390807],
+ [0.007943647847477694],
+ [0.02003764925766833],
+ [0.009573812850750063],
+ [0.01702713237376286],
+ [0.007153685002693248],
+ [0.01676942064321455],
+ [0.008012281919357385],
+ [0.01424993228754379],
+ [0.005986887554352669],
+ [0.01704799882132915],
+ [0.008145384126471394],
+ [0.01448665603962682],
+ [0.006086343359234239],
+ [0.02428557790460417],
+ [0.01160343585423386],
+ [0.0206368394035431],
+ [0.008670247303157035],
+ [0.01086675715317312],
+ [0.008119790817560615],
+ [0.01903413243710357],
+ [0.009094341326464849],
+ [0.01617438694822276],
+ [0.006795417266946891],
+ [0.009245418998841326],
+ [0.01644308026470771],
+ [0.006908304587387538],
+ [0.02756534742509875],
+ [0.0131704809291841],
+ [0.02342384645525713],
+ [0.009841164995614077]
+ ],
+ "Log Likelihood":-535.0231503100108,
+ "Rate Distributions":{
+ "non-synonymous/synonymous rate ratio for *background*": [
+[0.2330662032673943, 1]
+ ],
+ "non-synonymous/synonymous rate ratio for *test*": [
+[0.0543349869082771, 1]
+ ]
+ },
+ "display order":1,
+ "estimated parameters":28
+ },
+ "Nucleotide GTR":{
+ "AIC-c":1165.694393932368,
+ "Equilibrium frequencies": [
+[0.3348148148148147],
+ [0.202962962962963],
+ [0.2462962962962963],
+ [0.2159259259259259]
+ ],
+ "Log Likelihood":-559.6409189392783,
+ "Rate Distributions":{
+ "Substitution rate from nucleotide A to nucleotide C":0.1057602468701381,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0,
+ "Substitution rate from nucleotide C to nucleotide G":0.1465960735122673,
+ "Substitution rate from nucleotide C to nucleotide T":2.269319946484975,
+ "Substitution rate from nucleotide G to nucleotide T":0.1391184331291334
+ },
+ "display order":0,
+ "estimated parameters":23
+ }
+ },
+ "input":{
+ "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/a3/7f92afc4ab3867f3c9f3835478bffe/capsid_protein_C-nodups.fasta",
+ "number of sequences":9,
+ "number of sites":100,
+ "partition count":1,
+ "trees":{
+ "0":"(PP563828_1_2023_09_04,PP563831_1_2023_08_29,PP563880_1_2023_10_05,((PP564823_1_2023_10_06,PP563845_1_2023_10_22)Node4,(PP563884_1_2023_09_24,PP563838_1_2023_09_30,PP563839_1_2023_09_29)Node7)Node3,PP563832_1_2023_08_28)"
+ }
+ },
+ "model":{
+ "Q": [
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+ ],
+ "alphabet": [
+["AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT", "TAC", "TAT", "TCA", "TCC", "TCG", "TCT", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"]
+ ],
+ "ordering":{
+ "Factor I bipolar":0,
+ "Factor II secondary structure":1,
+ "Factor III volume":2,
+ "Factor IV composition":3,
+ "Factor V charge":4
+ },
+ "parameters":{
+ "lambda_Factor_III_volume":"Factor III volume",
+ "lambda_Factor_II_secondary_structure":"Factor II secondary structure",
+ "lambda_Factor_IV_composition":"Factor IV composition",
+ "lambda_Factor_I_bipolar":"Factor I bipolar",
+ "lambda_Factor_V_charge":"Factor V charge"
+ },
+ "residue_properties":{
+ "Factor I bipolar":{
+ "A":-0.6038471648233061,
+ "C":-1.372194149505415,
+ "D":1.072824912122625,
+ "E":1.38649848166705,
+ "F":-1.027868439614629,
+ "G":-0.3923473964334172,
+ "H":0.3433039718792401,
+ "I":-1.265933396304698,
+ "K":1.870802299139549,
+ "L":-1.041151033764719,
+ "M":-0.6774123016545719,
+ "N":0.9655424209103626,
+ "P":0.1931084841820725,
+ "Q":0.9512380887487276,
+ "R":1.571433061756759,
+ "S":-0.2329562666323415,
+ "T":-0.03269561636945143,
+ "V":-1.366063721436143,
+ "W":-0.6079341168694875,
+ "Y":0.2656518830017929
+ },
+ "Factor II secondary structure":{
+ "A":-1.330232386778897,
+ "C":0.475221663023938,
+ "D":0.3086744020630652,
+ "E":-1.48451849969357,
+ "F":-0.6027376027044098,
+ "G":1.688053557260477,
+ "H":-0.4259727183717044,
+ "I":-0.5588018222055293,
+ "K":-0.5731064949260951,
+ "L":-1.008377250566167,
+ "M":-1.557063625633582,
+ "N":0.8461213914214641,
+ "P":2.126389599912099,
+ "Q":-0.1827932821220867,
+ "R":-0.05609475231136144,
+ "S":1.42954768595311,
+ "T":0.3331966981554637,
+ "V":-0.2849695158404135,
+ "W":0.009298037268367709,
+ "Y":0.8481649160958307
+ },
+ "Factor III volume":{
+ "A":-0.3445293132340136,
+ "C":-0.4051709852318138,
+ "D":-1.718603788036881,
+ "E":0.6943706488988424,
+ "F":0.8889881078685267,
+ "G":0.6252673482501864,
+ "H":-0.7864143650009298,
+ "I":1.001809823213271,
+ "K":0.2506052352095138,
+ "L":-0.7074391642596085,
+ "M":1.043177785506344,
+ "N":0.6106945433514901,
+ "P":-0.7652602933737901,
+ "Q":-1.412574885164262,
+ "R":0.7061229109139199,
+ "S":-2.237583678622706,
+ "T":1.040357242622726,
+ "V":-0.2556822124000274,
+ "W":0.315947812013345,
+ "Y":1.455917227475868
+ },
+ "Factor IV composition":{
+ "A":1.630293655002852,
+ "C":-1.059000381337118,
+ "D":-0.2688255698874202,
+ "E":0.1174359673783979,
+ "F":-0.4121161401634496,
+ "G":1.08516648547448,
+ "H":-1.530405590795939,
+ "I":0.4081704577935299,
+ "K":-0.2875156442712501,
+ "L":1.314639065409281,
+ "M":-1.043425319350593,
+ "N":-0.1753751979682707,
+ "P":0.4372439068350431,
+ "Q":-0.5221799115348923,
+ "R":0.4569723186846413,
+ "S":0.6957899358113568,
+ "T":0.942914252664219,
+ "V":1.289718966230841,
+ "W":-2.209478293408426,
+ "Y":-0.8700229625672823
+ },
+ "Factor V charge":{
+ "A":-0.09353709405505788,
+ "C":-0.1633935055110449,
+ "D":-2.077715533208598,
+ "E":-0.5363882896154895,
+ "F":0.2640764618388941,
+ "G":1.322817670327799,
+ "H":-0.0499569474586623,
+ "I":0.5229938033821855,
+ "K":1.056209714679261,
+ "L":-0.5844546277732787,
+ "M":0.7767840688553127,
+ "N":0.5979772909083368,
+ "P":-0.8920791919831299,
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+ "translation-table":{
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+ "AAG":"K",
+ "AAT":"N",
+ "ACA":"T",
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+ "CAT":"H",
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+ "CCT":"P",
+ "CGA":"R",
+ "CGC":"R",
+ "CGG":"R",
+ "CGT":"R",
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+ "CTG":"L",
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+ "GAA":"E",
+ "GAC":"D",
+ "GAG":"E",
+ "GAT":"D",
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+ "GCC":"A",
+ "GCG":"A",
+ "GCT":"A",
+ "GGA":"G",
+ "GGC":"G",
+ "GGG":"G",
+ "GGT":"G",
+ "GTA":"V",
+ "GTC":"V",
+ "GTG":"V",
+ "GTT":"V",
+ "TAA":"X",
+ "TAC":"Y",
+ "TAG":"X",
+ "TAT":"Y",
+ "TCA":"S",
+ "TCC":"S",
+ "TCG":"S",
+ "TCT":"S",
+ "TGA":"X",
+ "TGC":"C",
+ "TGG":"W",
+ "TGT":"C",
+ "TTA":"L",
+ "TTC":"F",
+ "TTG":"L",
+ "TTT":"F"
+ }
+ },
+ "runtime":"2.5.70",
+ "tested":{
+ "0":{
+ "Node3":"test",
+ "Node4":"test",
+ "Node7":"test",
+ "PP563828_1_2023_09_04":"background",
+ "PP563831_1_2023_08_29":"background",
+ "PP563832_1_2023_08_28":"background",
+ "PP563838_1_2023_09_30":"background",
+ "PP563839_1_2023_09_29":"background",
+ "PP563845_1_2023_10_22":"background",
+ "PP563880_1_2023_10_05":"background",
+ "PP563884_1_2023_09_24":"background",
+ "PP564823_1_2023_10_06":"background"
+ }
+ },
+ "timers":{
+ "Model fitting":{
+ "order":1,
+ "timer":1
+ },
+ "PRIME analysis":{
+ "order":2,
+ "timer":32
+ },
+ "Total time":{
+ "order":0,
+ "timer":33
+ }
+ }
+}
diff --git a/tools/drhip/test-data/PRIME/gene2.json b/tools/drhip/test-data/PRIME/gene2.json
new file mode 100644
index 00000000000..77b1a75a376
--- /dev/null
+++ b/tools/drhip/test-data/PRIME/gene2.json
@@ -0,0 +1,791 @@
+{
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+ ]
+ },
+ "headers": [
+["α", "Synonymous substitution rate at a site"],
+ ["β", "Property independent non-synonymous rate a site"],
+ ["FEL α", "Synonymous substitution rate at a site (FEL model)"],
+ ["FEL β", "Log of property independent non-synonymous rate a site"],
+ ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
+ ["# subs", "The number of amino-acid substitutions that occurred at this site"],
+ ["# aa", "The number of unique amino-acids occurring at that site"],
+ ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
+ ["FEL LogL", "Site Log-likelihood under the FEL model"],
+ ["p-value", "Omnibus q-value (any property is important)"],
+ ["q-value", "Importance for Factor I bipolar"],
+ ["λ1", "p-value for non-zero effect of Factor I bipolar"],
+ ["p1", "Log likelihood when there is no effect of Factor I bipolar"],
+ ["LogL1", "Importance for Factor II secondary structure"],
+ ["λ2", "p-value for non-zero effect of Factor II secondary structure"],
+ ["p2", "Log likelihood when there is no effect of Factor II secondary structure"],
+ ["LogL2", "Importance for Factor III volume"],
+ ["λ3", "p-value for non-zero effect of Factor III volume"],
+ ["p3", "Log likelihood when there is no effect of Factor III volume"],
+ ["LogL3", "Importance for Factor IV composition"],
+ ["λ4", "p-value for non-zero effect of Factor IV composition"],
+ ["p4", "Log likelihood when there is no effect of Factor IV composition"],
+ ["LogL4", "Importance for Factor V charge"],
+ ["λ5", "p-value for non-zero effect of Factor V charge"],
+ ["p5", "Log likelihood when there is no effect of Factor V charge"],
+ ["LogL5", "0"]
+ ],
+ "substitutions":{
+ "0":{
+ "0":null,
+ "1":null,
+ "10":null,
+ "11":null,
+ "12":null,
+ "13":null,
+ "14":null,
+ "15":null,
+ "16":null,
+ "17":null,
+ "18":null,
+ "19":null,
+ "2":null,
+ "20":null,
+ "21":null,
+ "22":null,
+ "23":null,
+ "24":null,
+ "25":{
+ "PP564823_1_2023_10_06":"GGT",
+ "root":"GTT"
+ },
+ "26":{
+ "Node2":"TCA",
+ "Node3":"CCA",
+ "PP564823_1_2023_10_06":"TCA",
+ "root":"CCA"
+ },
+ "27":null,
+ "28":null,
+ "29":null,
+ "3":null,
+ "30":null,
+ "31":null,
+ "32":null,
+ "33":null,
+ "34":{
+ "PP563831_1_2023_08_29":"GAA",
+ "root":"AAA"
+ },
+ "35":null,
+ "36":null,
+ "37":{
+ "Node8":"CTT",
+ "root":"CTC"
+ },
+ "38":null,
+ "39":null,
+ "4":{
+ "Node2":"CGG",
+ "PP564823_1_2023_10_06":"CGG",
+ "root":"CGA"
+ },
+ "40":{
+ "Node2":"CAG",
+ "root":"CAA"
+ },
+ "41":null,
+ "42":null,
+ "43":null,
+ "44":null,
+ "45":{
+ "PP564823_1_2023_10_06":"ATG",
+ "root":"CTG"
+ },
+ "46":null,
+ "47":null,
+ "48":null,
+ "49":{
+ "Node3":"TTT",
+ "root":"TTC"
+ },
+ "5":{
+ "PP564823_1_2023_10_06":"AAG",
+ "root":"AAA"
+ },
+ "50":null,
+ "51":null,
+ "52":null,
+ "53":null,
+ "54":null,
+ "55":{
+ "Node2":"TTC",
+ "root":"TTT"
+ },
+ "56":null,
+ "57":null,
+ "58":null,
+ "59":{
+ "Node3":"CCT",
+ "root":"CCC"
+ },
+ "6":null,
+ "60":null,
+ "61":null,
+ "62":null,
+ "63":{
+ "Node2":"GGG",
+ "root":"GGA"
+ },
+ "64":null,
+ "65":null,
+ "66":null,
+ "67":null,
+ "68":null,
+ "69":{
+ "Node2":"GGT",
+ "PP564823_1_2023_10_06":"AGC",
+ "root":"GGC"
+ },
+ "7":null,
+ "70":null,
+ "71":null,
+ "72":null,
+ "73":null,
+ "74":null,
+ "75":null,
+ "76":null,
+ "77":null,
+ "78":null,
+ "79":null,
+ "8":{
+ "PP564823_1_2023_10_06":"GGT",
+ "root":"GCT"
+ },
+ "80":{
+ "PP563838_1_2023_09_30":"CTG",
+ "PP564823_1_2023_10_06":"TTA",
+ "root":"CTA"
+ },
+ "81":null,
+ "82":null,
+ "83":{
+ "PP563832_1_2023_08_28":"TTT",
+ "root":"TTC"
+ },
+ "84":{
+ "PP564823_1_2023_10_06":"AAA",
+ "root":"AAG"
+ },
+ "85":null,
+ "86":{
+ "PP564823_1_2023_10_06":"GAG",
+ "root":"GAA"
+ },
+ "87":null,
+ "88":null,
+ "89":null,
+ "9":null,
+ "90":null,
+ "91":{
+ "Node2":"CTG",
+ "PP564823_1_2023_10_06":"CTG",
+ "root":"TTG"
+ },
+ "92":{
+ "PP564823_1_2023_10_06":"AAC",
+ "root":"AAT"
+ },
+ "93":null,
+ "94":null,
+ "95":{
+ "PP564823_1_2023_10_06":"AAC",
+ "root":"AAT"
+ },
+ "96":{
+ "PP564823_1_2023_10_06":"AGG",
+ "root":"AGA"
+ },
+ "97":null,
+ "98":null,
+ "99":null
+ }
+ }
+ },
+ "analysis":{
+ "authors":"Sergei L. Kosakovsky Pond",
+ "citation":"TBD",
+ "contact":"spond@temple.edu",
+ "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
+ "requirements":"in-frame codon alignment and a phylogenetic tree",
+ "residue_properties":null,
+ "version":"0.2.0"
+ },
+ "branch attributes":{
+ "0":{
+ "Node2":{
+ "Global MG94xREV":0.0155536653271895,
+ "Nucleotide GTR":0.01391650578382423
+ },
+ "Node3":{
+ "Global MG94xREV":0.007028463160179066,
+ "Nucleotide GTR":0.007313844682570613
+ },
+ "Node8":{
+ "Global MG94xREV":0.006625904948639312,
+ "Nucleotide GTR":0.006196659368038242
+ },
+ "PP563830_1_2023_09_02":{
+ "Global MG94xREV":0,
+ "Nucleotide GTR":1e-06,
+ "original name":"PP563830_1_2023_09_02"
+ },
+ "PP563831_1_2023_08_29":{
+ "Global MG94xREV":0.003308074904952416,
+ "Nucleotide GTR":0.003339882520232537,
+ "original name":"PP563831_1_2023_08_29"
+ },
+ "PP563832_1_2023_08_28":{
+ "Global MG94xREV":0.003305744077013286,
+ "Nucleotide GTR":0.003342518270787742,
+ "original name":"PP563832_1_2023_08_28"
+ },
+ "PP563838_1_2023_09_30":{
+ "Global MG94xREV":0.003316134050292535,
+ "Nucleotide GTR":0.003339882520180704,
+ "original name":"PP563838_1_2023_09_30"
+ },
+ "PP563839_1_2023_09_29":{
+ "Global MG94xREV":0,
+ "Nucleotide GTR":1e-06,
+ "original name":"PP563839_1_2023_09_29"
+ },
+ "PP563845_1_2023_10_22":{
+ "Global MG94xREV":0.005917829644775162,
+ "Nucleotide GTR":0.007157676157708746,
+ "original name":"PP563845_1_2023_10_22"
+ },
+ "PP564823_1_2023_10_06":{
+ "Global MG94xREV":0.04452770118405119,
+ "Nucleotide GTR":0.04195089101557686,
+ "original name":"PP564823_1_2023_10_06"
+ }
+ },
+ "attributes":{
+ "Global MG94xREV":{
+ "attribute type":"branch length",
+ "display order":1
+ },
+ "Nucleotide GTR":{
+ "attribute type":"branch length",
+ "display order":0
+ },
+ "original name":{
+ "attribute type":"node label",
+ "display order":-1
+ }
+ }
+ },
+ "data partitions":{
+ "0":{
+ "coverage": [
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
+ ],
+ "name":"prime.filter.default"
+ }
+ },
+ "fits":{
+ "Global MG94xREV":{
+ "AIC-c":1098.164186625619,
+ "Equilibrium frequencies": [
+[0.04022787530103862],
+ [0.01934493712337751],
+ [0.03425741450905353],
+ [0.01425856648080257],
+ [0.03379960463533115],
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+ [0.03434841386947805],
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+ [0.009623848489980729],
+ [0.0170426073132688],
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+ [0.01681485300040535],
+ [0.008085991904804354],
+ [0.0143192595888557],
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+ [0.01708787828271292],
+ [0.008217285364372072],
+ [0.0145517635478013],
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+ [0.02416007116849923],
+ [0.01161818898347029],
+ [0.02057432977490965],
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+ [0.01095174735555056],
+ [0.008072200842739543],
+ [0.01913496685581441],
+ [0.009201697278655068],
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+ [0.006782292004731834],
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+ [0.006892417094094173],
+ [0.02749367841825353],
+ [0.0132212670023302],
+ [0.02341317633368553],
+ [0.009744994946783913]
+ ],
+ "Log Likelihood":-522.0390026738794,
+ "Rate Distributions":{
+ "non-synonymous/synonymous rate ratio for *background*": [
+[0.2130897909742414, 1]
+ ],
+ "non-synonymous/synonymous rate ratio for *test*": [
+[0.05367176447095212, 1]
+ ]
+ },
+ "display order":1,
+ "estimated parameters":26
+ },
+ "Nucleotide GTR":{
+ "AIC-c":1130.795872905925,
+ "Equilibrium frequencies": [
+[0.3347619047619048],
+ [0.2033333333333333],
+ [0.2466666666666667],
+ [0.2152380952380952]
+ ],
+ "Log Likelihood":-546.2152441452704,
+ "Rate Distributions":{
+ "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0,
+ "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+ "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+ "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
+ },
+ "display order":0,
+ "estimated parameters":19
+ }
+ },
+ "input":{
+ "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/6a/8adfdc16ef877c493cc257d23c98ea/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
+ "number of sequences":7,
+ "number of sites":100,
+ "partition count":1,
+ "trees":{
+ "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
+ }
+ },
+ "model":{
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+ ],
+ "alphabet": [
+["AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT", "TAC", "TAT", "TCA", "TCC", "TCG", "TCT", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"]
+ ],
+ "ordering":{
+ "Factor I bipolar":0,
+ "Factor II secondary structure":1,
+ "Factor III volume":2,
+ "Factor IV composition":3,
+ "Factor V charge":4
+ },
+ "parameters":{
+ "lambda_Factor_III_volume":"Factor III volume",
+ "lambda_Factor_II_secondary_structure":"Factor II secondary structure",
+ "lambda_Factor_IV_composition":"Factor IV composition",
+ "lambda_Factor_I_bipolar":"Factor I bipolar",
+ "lambda_Factor_V_charge":"Factor V charge"
+ },
+ "residue_properties":{
+ "Factor I bipolar":{
+ "A":-0.6038471648233061,
+ "C":-1.372194149505415,
+ "D":1.072824912122625,
+ "E":1.38649848166705,
+ "F":-1.027868439614629,
+ "G":-0.3923473964334172,
+ "H":0.3433039718792401,
+ "I":-1.265933396304698,
+ "K":1.870802299139549,
+ "L":-1.041151033764719,
+ "M":-0.6774123016545719,
+ "N":0.9655424209103626,
+ "P":0.1931084841820725,
+ "Q":0.9512380887487276,
+ "R":1.571433061756759,
+ "S":-0.2329562666323415,
+ "T":-0.03269561636945143,
+ "V":-1.366063721436143,
+ "W":-0.6079341168694875,
+ "Y":0.2656518830017929
+ },
+ "Factor II secondary structure":{
+ "A":-1.330232386778897,
+ "C":0.475221663023938,
+ "D":0.3086744020630652,
+ "E":-1.48451849969357,
+ "F":-0.6027376027044098,
+ "G":1.688053557260477,
+ "H":-0.4259727183717044,
+ "I":-0.5588018222055293,
+ "K":-0.5731064949260951,
+ "L":-1.008377250566167,
+ "M":-1.557063625633582,
+ "N":0.8461213914214641,
+ "P":2.126389599912099,
+ "Q":-0.1827932821220867,
+ "R":-0.05609475231136144,
+ "S":1.42954768595311,
+ "T":0.3331966981554637,
+ "V":-0.2849695158404135,
+ "W":0.009298037268367709,
+ "Y":0.8481649160958307
+ },
+ "Factor III volume":{
+ "A":-0.3445293132340136,
+ "C":-0.4051709852318138,
+ "D":-1.718603788036881,
+ "E":0.6943706488988424,
+ "F":0.8889881078685267,
+ "G":0.6252673482501864,
+ "H":-0.7864143650009298,
+ "I":1.001809823213271,
+ "K":0.2506052352095138,
+ "L":-0.7074391642596085,
+ "M":1.043177785506344,
+ "N":0.6106945433514901,
+ "P":-0.7652602933737901,
+ "Q":-1.412574885164262,
+ "R":0.7061229109139199,
+ "S":-2.237583678622706,
+ "T":1.040357242622726,
+ "V":-0.2556822124000274,
+ "W":0.315947812013345,
+ "Y":1.455917227475868
+ },
+ "Factor IV composition":{
+ "A":1.630293655002852,
+ "C":-1.059000381337118,
+ "D":-0.2688255698874202,
+ "E":0.1174359673783979,
+ "F":-0.4121161401634496,
+ "G":1.08516648547448,
+ "H":-1.530405590795939,
+ "I":0.4081704577935299,
+ "K":-0.2875156442712501,
+ "L":1.314639065409281,
+ "M":-1.043425319350593,
+ "N":-0.1753751979682707,
+ "P":0.4372439068350431,
+ "Q":-0.5221799115348923,
+ "R":0.4569723186846413,
+ "S":0.6957899358113568,
+ "T":0.942914252664219,
+ "V":1.289718966230841,
+ "W":-2.209478293408426,
+ "Y":-0.8700229625672823
+ },
+ "Factor V charge":{
+ "A":-0.09353709405505788,
+ "C":-0.1633935055110449,
+ "D":-2.077715533208598,
+ "E":-0.5363882896154895,
+ "F":0.2640764618388941,
+ "G":1.322817670327799,
+ "H":-0.0499569474586623,
+ "I":0.5229938033821855,
+ "K":1.056209714679261,
+ "L":-0.5844546277732787,
+ "M":0.7767840688553127,
+ "N":0.5979772909083368,
+ "P":-0.8920791919831299,
+ "Q":-1.187526950526341,
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+ "W":-0.1178907053883378,
+ "Y":0.9690494214864698
+ }
+ },
+ "translation-table":{
+ "AAA":"K",
+ "AAC":"N",
+ "AAG":"K",
+ "AAT":"N",
+ "ACA":"T",
+ "ACC":"T",
+ "ACG":"T",
+ "ACT":"T",
+ "AGA":"R",
+ "AGC":"S",
+ "AGG":"R",
+ "AGT":"S",
+ "ATA":"I",
+ "ATC":"I",
+ "ATG":"M",
+ "ATT":"I",
+ "CAA":"Q",
+ "CAC":"H",
+ "CAG":"Q",
+ "CAT":"H",
+ "CCA":"P",
+ "CCC":"P",
+ "CCG":"P",
+ "CCT":"P",
+ "CGA":"R",
+ "CGC":"R",
+ "CGG":"R",
+ "CGT":"R",
+ "CTA":"L",
+ "CTC":"L",
+ "CTG":"L",
+ "CTT":"L",
+ "GAA":"E",
+ "GAC":"D",
+ "GAG":"E",
+ "GAT":"D",
+ "GCA":"A",
+ "GCC":"A",
+ "GCG":"A",
+ "GCT":"A",
+ "GGA":"G",
+ "GGC":"G",
+ "GGG":"G",
+ "GGT":"G",
+ "GTA":"V",
+ "GTC":"V",
+ "GTG":"V",
+ "GTT":"V",
+ "TAA":"X",
+ "TAC":"Y",
+ "TAG":"X",
+ "TAT":"Y",
+ "TCA":"S",
+ "TCC":"S",
+ "TCG":"S",
+ "TCT":"S",
+ "TGA":"X",
+ "TGC":"C",
+ "TGG":"W",
+ "TGT":"C",
+ "TTA":"L",
+ "TTC":"F",
+ "TTG":"L",
+ "TTT":"F"
+ }
+ },
+ "runtime":"2.5.73",
+ "tested":{
+ "0":{
+ "Node2":"test",
+ "Node3":"test",
+ "Node8":"test",
+ "PP563830_1_2023_09_02":"background",
+ "PP563831_1_2023_08_29":"background",
+ "PP563832_1_2023_08_28":"background",
+ "PP563838_1_2023_09_30":"background",
+ "PP563839_1_2023_09_29":"background",
+ "PP563845_1_2023_10_22":"background",
+ "PP564823_1_2023_10_06":"background"
+ }
+ },
+ "timers":{
+ "Model fitting":{
+ "order":1,
+ "timer":0
+ },
+ "PRIME analysis":{
+ "order":2,
+ "timer":41
+ },
+ "Total time":{
+ "order":0,
+ "timer":43
+ }
+ }
+}
diff --git a/tools/drhip/test-data/RELAX/gene2.json b/tools/drhip/test-data/RELAX/gene2.json
new file mode 100644
index 00000000000..978a26d5f19
--- /dev/null
+++ b/tools/drhip/test-data/RELAX/gene2.json
@@ -0,0 +1,476 @@
+{
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+ ],
+ "analysis":{
+ "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution g",
+ "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",
+ "contact":"spond@temple.edu",
+ "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems. \n Version 3 provides support for >2 branch sets.\n Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword support.\n Version 3.1.1 adds some bug fixes for better convergence.\n Version 4.0 adds support for synonymous rate variation.\n Version 4.1 adds further support for multiple hit models.\n Version 4.1.1 adds reporting for convergence diagnostics.\n Version 4.5 adds support for multiple datasets for joint testing.",
+ "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)",
+ "settings":{
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+ "convergence-unstable-alernative": [
+[1, -522.6676498161135]
+ ]
+ },
+ "version":"4.5"
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+ "branch attributes":{
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+ "RELAX partitioned descriptive":0.01559876567211344,
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+ "RELAX partitioned descriptive":0.006517288390096835,
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+ },
+ "PP563830_1_2023_09_02":{
+ "General descriptive":0,
+ "MG94xREV with separate rates for branch sets":0,
+ "Nucleotide GTR":1e-06,
+ "RELAX alternative":0,
+ "RELAX null":0,
+ "RELAX partitioned descriptive":0,
+ "k (general descriptive)":0.142259336825735,
+ "original name":"PP563830_1_2023_09_02"
+ },
+ "PP563831_1_2023_08_29":{
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+ "RELAX partitioned descriptive":0.003308741202209799,
+ "k (general descriptive)":0,
+ "original name":"PP563831_1_2023_08_29"
+ },
+ "PP563832_1_2023_08_28":{
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+ "MG94xREV with separate rates for branch sets":0.003308960225557515,
+ "Nucleotide GTR":0.003342518270787742,
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+ "RELAX partitioned descriptive":0.003304063756411897,
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+ "original name":"PP563832_1_2023_08_28"
+ },
+ "PP563838_1_2023_09_30":{
+ "General descriptive":9.013608661743278e+20,
+ "MG94xREV with separate rates for branch sets":0.003323149228197305,
+ "Nucleotide GTR":0.003339882520180704,
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+ "RELAX partitioned descriptive":0.003324464998291851,
+ "k (general descriptive)":5.780662618885804,
+ "original name":"PP563838_1_2023_09_30"
+ },
+ "PP563839_1_2023_09_29":{
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+ "MG94xREV with separate rates for branch sets":0,
+ "Nucleotide GTR":1e-06,
+ "RELAX alternative":0,
+ "RELAX null":0,
+ "RELAX partitioned descriptive":0,
+ "k (general descriptive)":0.1425590658406654,
+ "original name":"PP563839_1_2023_09_29"
+ },
+ "PP563845_1_2023_10_22":{
+ "General descriptive":104928730585.8187,
+ "MG94xREV with separate rates for branch sets":0.006280613182962003,
+ "Nucleotide GTR":0.007157676157708746,
+ "RELAX alternative":0.005843495996118961,
+ "RELAX null":0.006208117989454296,
+ "RELAX partitioned descriptive":0.005863420827271293,
+ "k (general descriptive)":3.662303477073882,
+ "original name":"PP563845_1_2023_10_22"
+ },
+ "PP564823_1_2023_10_06":{
+ "General descriptive":0.04402715605730399,
+ "MG94xREV with separate rates for branch sets":0.0452323709970251,
+ "Nucleotide GTR":0.04195089101557686,
+ "RELAX alternative":0.04787554162020877,
+ "RELAX null":0.04717582631948587,
+ "RELAX partitioned descriptive":0.04784408019616278,
+ "k (general descriptive)":0.1385670152460595,
+ "original name":"PP564823_1_2023_10_06"
+ }
+ },
+ "attributes":{
+ "General descriptive":{
+ "attribute type":"branch length",
+ "display order":4
+ },
+ "MG94xREV with separate rates for branch sets":{
+ "attribute type":"branch length",
+ "display order":1
+ },
+ "Nucleotide GTR":{
+ "attribute type":"branch length",
+ "display order":0
+ },
+ "RELAX alternative":{
+ "attribute type":"branch length",
+ "display order":2
+ },
+ "RELAX null":{
+ "attribute type":"branch length",
+ "display order":3
+ },
+ "RELAX partitioned descriptive":{
+ "attribute type":"branch length",
+ "display order":5
+ },
+ "k (general descriptive)":{
+ "attribute type":"branch label",
+ "display order":4
+ },
+ "original name":{
+ "attribute type":"node label",
+ "display order":-1
+ }
+ }
+ },
+ "data partitions":{
+ "0":{
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+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
+ ],
+ "name":"relax.filter.default"
+ }
+ },
+ "fits":{
+ "General descriptive":{
+ "AIC-c":1118.913606609998,
+ "Log Likelihood":-518.0931669413627,
+ "Rate Distributions":{
+ "Shared":{
+ "0":{
+ "omega":7.360820659190173e-05,
+ "proportion":0.9977887157539754
+ },
+ "1":{
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+ "proportion":0.002196242211009209
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+ "2":{
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+ "proportion":1.504203501536015e-05
+ }
+ }
+ },
+ "display order":4,
+ "estimated parameters":39
+ },
+ "MG94xREV with separate rates for branch sets":{
+ "AIC-c":1099.34487709039,
+ "Equilibrium frequencies": [
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+ [0.009744994946783913]
+ ],
+ "Log Likelihood":-522.6293479062649,
+ "Rate Distributions":{
+ "non-synonymous/synonymous rate ratio for *Reference*": [
+[0.1357990297446096, 1]
+ ],
+ "non-synonymous/synonymous rate ratio for *Test*": [
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+ ]
+ },
+ "display order":1,
+ "estimated parameters":26
+ },
+ "Nucleotide GTR":{
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+ "Equilibrium frequencies": [
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+ [0.2033333333333333],
+ [0.2466666666666667],
+ [0.2152380952380952]
+ ],
+ "Log Likelihood":-546.2152441452704,
+ "Rate Distributions":{
+ "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+ "Substitution rate from nucleotide A to nucleotide G":1,
+ "Substitution rate from nucleotide A to nucleotide T":0,
+ "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+ "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+ "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
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+ "estimated parameters":19
+ },
+ "RELAX alternative":{
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+ "Log Likelihood":-522.4505686547367,
+ "Rate Distributions":{
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+ },
+ "Synonymous site-to-site rates":{
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+ "rate":0
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+ "1":{
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+ "Test":{
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+ "display order":2,
+ "estimated parameters":35
+ },
+ "RELAX null":{
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+ "Log Likelihood":-522.6676332581309,
+ "Rate Distributions":{
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+ "1":{
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+ },
+ "Synonymous site-to-site rates":{
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+ "rate":0
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+ "1":{
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+ "Test":{
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+ "display order":3,
+ "estimated parameters":34
+ },
+ "RELAX partitioned descriptive":{
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+ "Log Likelihood":-522.4504745703164,
+ "Rate Distributions":{
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+ "proportion":0
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+ }
+ },
+ "display order":5,
+ "estimated parameters":39
+ }
+ },
+ "input":{
+ "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/f1/b617f0d3def2dbef497adeeb300f64/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
+ "number of sequences":7,
+ "number of sites":100,
+ "partition count":1,
+ "trees":{
+ "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
+ }
+ },
+ "runtime":"2.5.73",
+ "test results":{
+ "LRT":0.4341292067883842,
+ "p-value":0.5099697340837581,
+ "relaxation or intensification parameter":0.459831450191493
+ },
+ "tested":{
+ "0":{
+ "Node2":"Reference",
+ "Node3":"Reference",
+ "Node8":"Test",
+ "PP563830_1_2023_09_02":"Reference",
+ "PP563831_1_2023_08_29":"Reference",
+ "PP563832_1_2023_08_28":"Reference",
+ "PP563838_1_2023_09_30":"Reference",
+ "PP563839_1_2023_09_29":"Reference",
+ "PP563845_1_2023_10_22":"Reference",
+ "PP564823_1_2023_10_06":"Reference"
+ }
+ },
+ "timers":{
+ "General descriptive model fitting":{
+ "order":2,
+ "timer":15
+ },
+ "Overall":{
+ "order":0,
+ "timer":44
+ },
+ "Preliminary model fitting":{
+ "order":1,
+ "timer":1
+ },
+ "RELAX alternative model fitting":{
+ "order":3,
+ "timer":22
+ },
+ "RELAX null model fitting":{
+ "order":4,
+ "timer":3
+ },
+ "RELAX partitioned descriptive":{
+ "order":5,
+ "timer":3
+ }
+ }
+}