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research:package_content [2017/07/11 13:39] – sean | research:package_content [2017/09/23 18:42] (current) – sean |
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==== Evo-SS-Package_content ==== | ==== Evo-SS-Package_content ==== |
''├── _README.txt (README for "Evo-SS-Package")\\ | |
| [[:evoss|Back to the Evo-SS-Package]] |
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| ├── _README.txt (README for "Evo-SS-Package")\\ |
├── _util/ (Scripts and library, categorized by folders)\\ | ├── _util/ (Scripts and library, categorized by folders)\\ |
│ ├── ASSR/ (Ancestral secondary structure reconstruction related)\\ | │ ├── ASSR/ (Ancestral secondary structure reconstruction related)\\ |
│ │ ├── CharVector2JavaArray.m\\ | │ │ ├── CharVector2JavaArray.m\\ |
│ │ └── SetTransitionProb.m\\ | │ │ └── SetTransitionProb.m\\ |
│ ├── JAR/\\ | │ ├── JAR/ |
│ │ └── NBbnkit.jar (Pre-compiled JAVA library for ASSR)\\ | │ │ └── NBbnkit.jar (Pre-compiled JAVA library for ASSR)\\ |
│ ├── MLDist/ (Evolutionary distance estimation by maximum likelihood)\\ | │ ├── MLDist/ (Evolutionary distance estimation by maximum likelihood)\\ |
│ │ ├── CombineOptimization02.m\\ | │ │ ├── CombineOptimization02.m\\ |
│ │ ├── CreatePhytreeFromBGraph.m\\ | │ │ ├── CreatePhytreeFromBGraph.m\\ |
│ │ ├── GetInitialDistanceByLeastSquare.m\\ | │ │ ├── GetInitialDistanceByLeastSquare.m\ |
│ │ ├── GetTipsLikelihood4SS.m\\ | │ │ ├── GetTipsLikelihood4SS.m\\ |
│ │ ├── GetTreeLikelihood03.m\\ | │ │ ├── GetTreeLikelihood03.m\\ |
│ │ ├── PHYML_SS03.m\\ | │ │ ├── PHYML_SS03.m\\ |
│ │ └── fminbnd_JSLai03.m\\ | │ │ └── fminbnd_JSLai03.m\\ |
│ └── Model/ (Amino acid, secondary structure models)\\ | │ └── Model/ (Amino acid, secondary structure models)\\ |
│ ├── Dayhoff.m\\ | │ ├── Dayhoff.m (Amino acid model, Dayhoff's)\\ |
│ ├── GetExpMByTime.m\\ | │ ├── GetExpMByTime.m (Script to calculate transition probabilities)\\ |
│ ├── JTT.m\\ | │ ├── JTT.m (Amino acid model, JTT)\\ |
│ └── SS7Label.m\\ | │ ├── SS7Label_JTT.m (Secondary structure model, alternative)\\ |
| │ └── SS7Label.m (Secondary structure model, Evo-SS)\\ |
├── Evo-SS-ASSR/ (ASSR scripts with an example)\\ | ├── Evo-SS-ASSR/ (ASSR scripts with an example)\\ |
| │ ├── _README.txt (Instruction to do Ancestral Secondary Structure Reconstruction in MATLAB)\\ |
│ ├── DoASSR.m (Major script to do ASSR)\\ | │ ├── DoASSR.m (Major script to do ASSR)\\ |
│ ├── Main.m\\ | │ ├── Main.m\\ |
│ ├── example_Wilson_MSSA.fasta (MSSA from Wilson case)\\ | │ ├── example_Wilson_MSSA.fasta (MSSA from Wilson case)\\ |
│ └── example_Wilson_PrunedTree.txt (Phylogenetic tree from Wilson case)\\ | │ └── example_Wilson_PrunedTree.txt (Phylogenetic tree from Wilson case)\\ |
├── Evo-SS-MLDist/ (Evolutionary distance estimation with examples)\\ | ├── Evo-SS-MLDist/ (Evolutionary distance estimation with examples)\\ |
| │ ├── _README.txt (Instruction to estimate pairwise distances in MATLAB)\\ |
│ ├── EstimateAADistance.m (Major script to estimate evolutionary distance based on JTT-AA model)\\ | │ ├── EstimateAADistance.m (Major script to estimate evolutionary distance based on JTT-AA model)\\ |
│ ├── EstimateSSDistance.m (Major script to estimate evolutionary distance based on Evo-SS model)\\ | │ ├── EstimateSSDistance.m (Major script to estimate evolutionary distance based on Evo-SS model)\\ |
│ └── example_PF00031_SS.fasta (Secondary structure example 1)\\ | │ └── example_PF00031_SS.fasta (Secondary structure example 1)\\ |
├── Evo-SS-StructML/ (Evolutionary tree construction)\\ | ├── Evo-SS-StructML/ (Evolutionary tree construction)\\ |
| │ ├── _README.txt (Instruction to build secondary structure tree in MATLAB)\\ |
│ ├── BuildSSTree.m (Major script to construct phylogenetic tree based on Evo-SS model)\\ | │ ├── BuildSSTree.m (Major script to construct phylogenetic tree based on Evo-SS model)\\ |
│ ├── Main.m\\ | │ ├── Main.m\\ |
│ └── example.fasta\\ | │ └── example.fasta\\ |
└── _Dataset/ (All datasets and model parameters. See "_Dataset/_README.txt for details");\\ | ├── Evo-SS-Boundary/ (Variation in secondary structure)\\ |
├── ASSR/ (ASSR-related dataset)\\ | │ ├── EvoSS_BoundaryTest1.m (Test boundaries between modern and actual, reconstructed ancestral protein)\\ |
├── Model/ (Evo-SS model)\\ | │ ├── EvoSS_BoundaryTest2.m (Test boundaries around within phylogenetic trees)\\ |
├── Pfam/ (MSA, MSSA from Pfam)\\ | │ └── Main.m\\ |
├── TIR_domains/ (TIR trees and dataset)\\ | └── _Dataset/ (All datasets and model parameters. See "_Dataset/_README.txt for details")\\ |
└── _README.txt''\ | ├── ASSR/ (ASSR-related dataset)\\ |
| ├── Model/ (Evo-SS model)\\ |
| ├── Pfam/ (MSA, MSSA from Pfam)\\ |
| ├── TIR_domains/ (TIR trees and dataset)\\ |
| └── _README.txt\\ |
| \\ |
| [[:evoss|Back to the Evo-SS-Package]] |
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