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--- research:package_content [2017/07/11 13:41] – 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)\\
 │   ├── ASSR/            (Ancestral secondary structure reconstruction related)\\
@@ Line 10: / Line 11: @@
 │   │   ├── CharVector2JavaArray.m\\
 │   │   └── SetTransitionProb.m\\
-│   ├── JAR/\\
+│   ├── JAR/
 │   │   └── NBbnkit.jar  (Pre-compiled JAVA library for ASSR)\\
 │   ├── MLDist/          (Evolutionary distance estimation by maximum likelihood)\\
@@ Line 18: / Line 19: @@
 │   │   ├── CombineOptimization02.m\\
 │   │   ├── CreatePhytreeFromBGraph.m\\
-│   │   ├── GetInitialDistanceByLeastSquare.m\\
+│   │   ├── GetInitialDistanceByLeastSquare.m\
 │   │   ├── GetTipsLikelihood4SS.m\\
 │   │   ├── GetTreeLikelihood03.m\\
@@ Line 26: / Line 27: @@
 │   │   ├── PHYML_SS03.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)\\
+│   ├── _README.txt              (Instruction to do Ancestral Secondary Structure Reconstruction in MATLAB)\\
 │   ├── DoASSR.m                 (Major script to do ASSR)\\
 │   ├── Main.m\\
 │   ├── example_Wilson_MSSA.fasta      (MSSA 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)\\
 │   ├── EstimateSSDistance.m     (Major script to estimate evolutionary distance based on Evo-SS model)\\
@@ Line 45: / Line 49: @@
 │   └── example_PF00031_SS.fasta (Secondary structure example 1)\\
 ├── 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)\\
 │   ├── Main.m\\
 │   └── 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\\
 \\
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