Show pageOld revisionsBacklinksBack to top This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong. ==== 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\\ \\ [[:evoss|Back to the Evo-SS-Package]] research/package_content.txt Last modified: 2017/09/23 18:42by sean