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research:package_content [2017/07/11 13:38] – created sean | research:package_content [2017/09/23 18:42] (current) – sean |
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[[Evo-SS-Package_content]] | ==== Evo-SS-Package_content ==== |
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| [[: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)\\ |
| │ ├── 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\\ |
| \\ |
| [[:evoss|Back to the Evo-SS-Package]] |