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Evo-SS-Package_content
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├── _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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