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--- research:package_content [2017/09/23 18:41] – sean
+++ research:package_content [2017/09/23 18:42] (current) – sean
@@ Line 4: / Line 4: @@
-''
-├── _README.txt          (README for "Evo-SS-Package")
+├── _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)\\
-│   │   ├── ASR_SS03.m   (ASSR algorithm)
+│   │   ├── ASR_SS03.m   (ASSR algorithm)\\
-│   │   ├── CharVector2JavaArray.m
+│   │   ├── CharVector2JavaArray.m\\
-│   │   └── SetTransitionProb.m
+│   │   └── SetTransitionProb.m\\
 │   ├── 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)\\
-│   │   ├── ProteinDIST.m
+│   │   ├── ProteinDIST.m\\
-│   │   └── SS7LabelDIST.m
+│   │   └── SS7LabelDIST.m\\
-│   ├── StructML/          (Tree inference by maximum likelihood)
+│   ├── StructML/          (Tree inference by maximum likelihood)\\
-│   │   ├── CombineOptimization02.m
+│   │   ├── CombineOptimization02.m\\
-│   │   ├── CreatePhytreeFromBGraph.m
+│   │   ├── CreatePhytreeFromBGraph.m\\
-│   │   ├── GetInitialDistanceByLeastSquare.m
+│   │   ├── GetInitialDistanceByLeastSquare.m\
-│   │   ├── GetTipsLikelihood4SS.m
+│   │   ├── GetTipsLikelihood4SS.m\\
-│   │   ├── GetTreeLikelihood03.m
+│   │   ├── GetTreeLikelihood03.m\\
-│   │   ├── ImproveTree04.m
+│   │   ├── ImproveTree04.m\\
-│   │   ├── NNInterchange03.m
+│   │   ├── NNInterchange03.m\\
-│   │   ├── OptimizeSwap02.m
+│   │   ├── OptimizeSwap02.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        (Amino acid model, Dayhoff's)
+│       ├── Dayhoff.m        (Amino acid model, Dayhoff's)\\
-│       ├── GetExpMByTime.m  (Script to calculate transition probabilities)
+│       ├── GetExpMByTime.m  (Script to calculate transition probabilities)\\
-│       ├── JTT.m            (Amino acid model, JTT)
+│       ├── JTT.m            (Amino acid model, JTT)\\
-│       ├── SS7Label_JTT.m   (Secondary structure model, alternative)
+│       ├── SS7Label_JTT.m   (Secondary structure model, alternative)\\
-│       └── SS7Label.m       (Secondary structure model, Evo-SS)
+│       └── 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)
+│   ├── _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)
+│   ├── _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)\\
-│   ├── Main.m
+│   ├── Main.m\\
-│   ├── example_PF00017_AA.fasta (Amino acid example 1)
+│   ├── example_PF00017_AA.fasta (Amino acid example 1)\\
-│   ├── example_PF00017_SS.fasta (Secondary structure example 1)
+│   ├── example_PF00017_SS.fasta (Secondary structure example 1)\\
-│   ├── example_PF00031_AA.fasta (Amino acid example 2)
+│   ├── example_PF00031_AA.fasta (Amino acid example 2)\\
-│   └── 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)
+│   ├── _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\\
-├── Evo-SS-Boundary/             (Variation in secondary structure)
+├── Evo-SS-Boundary/             (Variation in secondary structure)\\
-│   ├── EvoSS_BoundaryTest1.m    (Test boundaries between modern and actual, reconstructed ancestral protein)
+│   ├── EvoSS_BoundaryTest1.m    (Test boundaries between modern and actual, reconstructed ancestral protein)\\
-│   ├── EvoSS_BoundaryTest2.m    (Test boundaries around within phylogenetic trees)
+│   ├── EvoSS_BoundaryTest2.m    (Test boundaries around within phylogenetic trees)\\
-│   └── Main.m
+│   └── Main.m\\
-└── _Dataset/         (All datasets and model parameters. See "_Dataset/_README.txt for details");
+└── _Dataset/         (All datasets and model parameters. See "_Dataset/_README.txt for details")\\
-    ├── ASSR/         (ASSR-related dataset)
+    ├── ASSR/         (ASSR-related dataset)\\
-    ├── Model/        (Evo-SS model)
+    ├── Model/        (Evo-SS model)\\
-    ├── Pfam/         (MSA, MSSA from Pfam)
+    ├── Pfam/         (MSA, MSSA from Pfam)\\
-    ├── TIR_domains/  (TIR trees and dataset)
+    ├── TIR_domains/  (TIR trees and dataset)\\
-    └── _README.txt
+    └── _README.txt\\
 \\
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