| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/ |
| H A D | ancestral.bf | 5 /** @module ancestral */
7 ancestral._ancestralRecoveryCache = {};
86 ancestral._bacCacheInstanceCounter = 0;
89 * Builds ancestral states
90 * @name ancestral.build
105 * @name ancestral._buildAncestralCacheInternal
248 /* an ancestral sequence */
308 * @name ancestral.ComputeSubstitutionCounts
348 * @name ancestral.Sequences
388 * @name ancestral.ComputeSubstitutionCounts
[all …]
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_TrickyVariantAncestralSelection.testenv/TrickyVariantAncestralSelection/ |
| H A D | root.sdf | 4 This museum case demonstrates how ancestral variant selections
7 The prim /Root/B/C has ancestral variant selections from references
8 /A/B/C and /B/C in ref2.sdf, as well as a non-ancestral selection
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_TrickyNestedClasses4.testenv/TrickyNestedClasses4/ |
| H A D | root.sdf | 4 This museum exhibits behavior involving nested classes and ancestral
7 source involve the same ancestral inherit arc between /Rig and
9 inherit arc. In this case, Pcp must expand the ancestral inherit arc
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_SubrootInheritsAndVariants.testenv/SubrootInheritsAndVariants/ |
| H A D | root.sdf | 40 # consistent with how we treat other ancestral arcs when propagating implied
45 # to another prim with an ancestral variant selection.
52 # Tests a bug previously encountered with ancestral variant selections. This
57 # /RootRef/Child's inherit of /Group/Model has an ancestral variant in that
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_SpecializesAndAncestralArcs.testenv/SpecializesAndAncestralArcs/ |
| H A D | root.sdf | 4 These test cases exercise the interactions between ancestral
22 Tests ancestral references and specializes.
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_ImpliedAndAncestralInherits.testenv/ImpliedAndAncestralInherits/ |
| H A D | CharGroupRig.sdf | 6 # prim index for Hand is processed, the ancestral inherit arc from includes is
9 # in turn caused the ancestral inherit arc from includes to be implied again.
46 # expect to cull the ancestral implied inherit nodes that are not needed.
|
| H A D | root.sdf | 7 # cull the ancestral implied inherits in the CharGroupRig.
|
| /dports/biology/phyml/phyml-3.3.20200621/src/ |
| H A D | Makefile.am | 131 ancestral.c ancestral.h\
277 ancestral.c ancestral.h\
315 ancestral.c ancestral.h\
351 ancestral.c ancestral.h\
387 ancestral.c ancestral.h\
555 ancestral.c ancestral.h\
595 ancestral.c ancestral.h\
695 ancestral.c ancestral.h \
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_BasicNestedPayload.testenv/BasicNestedPayload/ |
| H A D | root.sdf | 16 namespace, the strength ordering of ancestral payloads
19 where deeper opinions are stronger than ancestral
43 expressed within the ancestral payload.
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_SubrootReferenceAndVariants.testenv/SubrootReferenceAndVariants/ |
| H A D | root.sdf | 17 # Tests a bug previously encountered with ancestral variant selections.
20 # /RootRef/Child's reference to /Group/Model has an ancestral variant in that
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_TrickyVariantInPayload.testenv/TrickyVariantInPayload/ |
| H A D | root.sdf | 5 and ancestral payloads.
14 variant selection. Since ancestral payloads are stronger than
|
| /dports/biology/vcflib/vcflib-1.0.2/doc/ |
| H A D | genotypeSummary.md | 29 optional, a,ancestral -- describe counts relative to the ancestral allele defined as AA in INFO
|
| /dports/games/pcgen/pcgen/data/pathfinder/paizo/player_companion/dwarves_of_golarion/_pfs/ |
| H A D | _.pcc | 44 …ancestral communion, ancestral gift, bloodsworn retribution, dwarven veil, invigorating repose, mi…
|
| /dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/ |
| H A D | MG94-REV-Constrain-Branch-Lengths.bf | 25 // namespace 'alignments' for ancestral reconstruction functions
28 // namespace 'trees' for ancestral reconstruction functions
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
| H A D | BGM.bf | 8 LoadFunctionLibrary("libv3/tasks/ancestral.bf");
19 "BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to
251 io.ReportProgressMessageMD("bgm", "ancestral", "Performing joint ancestral state reconstruction and…
253 bgm.ancestral_cache = ancestral.build (bgm.baseline_fit[terms.likelihood_function], 0, None);
258 bgm.counts = ancestral.ComputeSubstitutionCounts(
266 bgm.counts = ancestral.ComputeSubstitutionCounts(
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpDependencies.testenv/BasicAncestralReference/ |
| H A D | root.sdf | 6 In addition, across A's reference (the ancestral reference)
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_BasicAncestralReference.testenv/BasicAncestralReference/ |
| H A D | root.sdf | 6 In addition, across A's reference (the ancestral reference)
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_TrickyNestedSpecializes2.testenv/TrickyNestedSpecializes2/ |
| H A D | root.sdf | 8 as stronger than the ancestral opinion from /Class_1.
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/SelectionAnalyses/ |
| H A D | SLAC.bf | 12 LoadFunctionLibrary("libv3/tasks/ancestral.bf");
30 uses a maximum likelihood ancestral state reconstruction
63 how many ancestral reconstruction replicates to run ;
97 KeywordArgument ("samples", "number of samples to assess ancestral reconstruction uncertainty", "1…
134 slac.samples = io.PromptUser ("\n>Select the number of samples used to assess ancestral reconstruct…
212 io.ReportProgressMessageMD("slac", "anc", "Performing joint maximum likelihood ancestral state reco…
250 …slac.ancestors = ancestral.build (slac.partitioned_mg_results[terms.likelihood_function], …
329 slac.sampled = ancestral.build (lf, partition, {"sample": TRUE});
344 …io.ReportAnalysisStageMD ("Generating `slac.samples` ancestral sequence samples to obtain confiden…
374 io.ReportProgressBar("", "Done with ancestral sampling \n");
|
| /dports/misc/usd/USD-21.11/pxr/usd/pcp/testenv/testPcpMuseum_BasicRelocateToAnimInterface.testenv/BasicRelocateToAnimInterface/ |
| H A D | charRig.sdf | 10 … scope has an additional relocation that must compose together with the ancestral relocation above…
|
| /dports/textproc/kibana7/kibana-7.16.2-darwin-x86_64/node_modules/mdast-add-list-metadata/node_modules/unist-util-visit-parents/ |
| H A D | readme.md | 3 [Unist][] node visitor, with ancestral information.
47 Visit nodes, with ancestral information. Optionally by node type.
|
| /dports/textproc/opensearch-dashboards/opensearch-dashboards-1.2.0-linux-x64/plugins/observabilityDashboards/node_modules/unist-util-visit-parents/ |
| H A D | readme.md | 3 [Unist][] node visitor, with ancestral information.
47 Visit nodes, with ancestral information. Optionally by node type.
|
| /dports/textproc/opensearch-dashboards/opensearch-dashboards-1.2.0-linux-x64/plugins/reportsDashboards/node_modules/unist-util-visit-parents/ |
| H A D | readme.md | 3 [Unist][] node visitor, with ancestral information.
47 Visit nodes, with ancestral information. Optionally by node type.
|
| /dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/ |
| H A D | function-loader.bf | 14 LoadFunctionLibrary("libv3/tasks/ancestral.bf");
|
| /dports/biology/mrbayes/MrBayes-3.2.7/ |
| H A D | NEWS | 32 * Improve the efficiency of moving ancestral fossils.
39 * Fix reporting ancestral states under GTR+I+G model.
|