==== Evo-SS-Package_content ====

[[:evoss|Back to the Evo-SS-Package]]



├── _README.txt          (README for "Evo-SS-Package")\\
├── _util/               (Scripts and library, categorized by folders)\\
│   ├── ASSR/            (Ancestral secondary structure reconstruction related)\\
│   │   ├── ASR_SS03.m   (ASSR algorithm)\\
│   │   ├── CharVector2JavaArray.m\\
│   │   └── SetTransitionProb.m\\
│   ├── JAR/
│   │   └── NBbnkit.jar  (Pre-compiled JAVA library for ASSR)\\
│   ├── MLDist/          (Evolutionary distance estimation by maximum likelihood)\\
│   │   ├── ProteinDIST.m\\
│   │   └── SS7LabelDIST.m\\
│   ├── StructML/          (Tree inference by maximum likelihood)\\
│   │   ├── CombineOptimization02.m\\
│   │   ├── CreatePhytreeFromBGraph.m\\
│   │   ├── GetInitialDistanceByLeastSquare.m\
│   │   ├── GetTipsLikelihood4SS.m\\
│   │   ├── GetTreeLikelihood03.m\\
│   │   ├── ImproveTree04.m\\
│   │   ├── NNInterchange03.m\\
│   │   ├── OptimizeSwap02.m\\
│   │   ├── PHYML_SS03.m\\
│   │   └── fminbnd_JSLai03.m\\
│   └── Model/               (Amino acid, secondary structure models)\\
│       ├── Dayhoff.m        (Amino acid model, Dayhoff's)\\
│       ├── GetExpMByTime.m  (Script to calculate transition probabilities)\\
│       ├── JTT.m            (Amino acid model, JTT)\\
│       ├── 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)\\
│   ├── _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)\\
│   ├── Main.m\\
│   ├── example_PF00017_AA.fasta (Amino acid example 1)\\
│   ├── example_PF00017_SS.fasta (Secondary structure example 1)\\
│   ├── example_PF00031_AA.fasta (Amino acid example 2)\\
│   └── 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\\
├── Evo-SS-Boundary/             (Variation in secondary structure)\\
│   ├── EvoSS_BoundaryTest1.m    (Test boundaries between modern and actual, reconstructed ancestral protein)\\
│   ├── EvoSS_BoundaryTest2.m    (Test boundaries around within phylogenetic trees)\\
│   └── Main.m\\
└── _Dataset/         (All datasets and model parameters. See "_Dataset/_README.txt for details")\\
    ├── 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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