Next:
List of Tables
Up:
The DARWIN Manual ©
Previous:
The DARWIN Manual ©
Contents
Contents
List of Tables
List of Figures
An Introduction to Darwin
Exploring the Basics
Initiating a Darwin Session
Basic Terminology and Arithmetic Operators
Comments
Variables
Simple types
Sets
Lists and Arrays
Strings
Built-in Functions for Sets, Arrays and string
Simple Output
Boolean Expressions
Decisions
Looping Around
Interrupting Computation
Ending a Darwin Session
Navigating Around the System
Advanced String Manipulation
Printing
printf
sprintf
Exact string Search
String Format Scan -
sscanf
Searching for Strings
Searching with SGML Tags
Approximate string Search
ApproxSearchString
BestSearchString
Procedures
The
proc
Command
Commenting a Procedure:
description
Scoping Rules
Independent Scopes
Examing Global Variables from within Routines
Modifying Global Variables
Modifying the Value of a Parameter
Functions
The
return
Command
Nested Routines
Variable Number of Arguments
Lists and Arrays Revisited
Zippable Commands
Sorting
Searching
Structured Types
Defining New Structured Types: An Example
Error Checking
Simplification
Normalization
Nested Types
Selection on Data Structures
The Types of Structured Types
Iteration and Recursion
Iteration
The
for
Command
The
while
Statement
Recursive Calls
Input/Output
Standard Files
The
ReadProgram
Command
The
ReadLibrary
command
The
save
Command
Raw Data Files
Reading Raw Data Files
Creating Raw Data Files
Initializing Your Darwin Session
Genetic Databases
Sequence Databases
Darwin Sequence Databases
Building a Darwin Sequence Database
Map Files and Patricia Trees
Accessing a Darwin Sequence Database
The
Entry
Structure
The
Offset
Structure
The
Sequence
Structure
The
String
Function
The
SearchDb
Function
Indexing a Darwin Sequence Database
References
Randomization, Statistics and Visualization
Randomization
Basic Visualization Functions
Set
(
plotoutput
)
Set
(
plotdevice
)
Creating Plots
Creating Dot Plots
Creating Histograms
Drawing Trees
Annotating Plots and Graphs
Statistics
Calculating an Exponential Fit
Linear Regressions
Single Value Decompositions
The
stats
command
The
UpdateStat
command
Generating Distributions
Smothing Data Points
Polymorphism
System Commands
Communicating with the Operating System
Date and Time
Operating System Commands
Garbage Collection
Internal Variables
Options
A Guide to Debugging
Tracing and the Print Level
printlevel
trace
Trapping Errors
Measuring Performance
option numeric
A Small Example
Producing HTML Code
Darwin's Interprocessor Skills
Calling External Functions
Darwin and Problems from Biochemistry
Point Accepted Mutations and Dayhoff Matrices
Modeling Evolution
Point Accepted Mutations
Dayhoff Matrices
Interpreting Scores
The Original Dayhoff Matrices
Better Dayhoff Matrices
The
CreateDayMatrices
Function
The
CreateDayMatrix
Function
Percent Identity and PAM Distance
Estimating Mutation Matrices
Other Similarity Matrices
Insertions and Deletions
Gap Probabilities and Penalties
The Pairwise Comparison of Amino Acid Sequences
Dynamic Programming
The
DynProg
Function
The
BackDynProg
Function
Global Alignments
The
Match
Structure
Matching Routines
The
GlobalAlign
Function
The
LocalAlign
Function
The
LogDelLocalRefine
Function
Estimating PAM Distances
The
FindBestPam
Function
The
LocalAlignBestPam
Function
The
DrawSimPam
Function
The
GetOffset
Function
Searching for Genes
Searching for hypothetical peptides
Direct nucleotide versus peptide alignment
All versus All
Phylogenetic Trees
Phylogenetic Trees
Introduction
Character-based Methods
Parsimony
Character Compatability
Distance-based Methods
Tree Generation
The Darwin Distance-based Algorithm for Phylogenetic Trees
Rooted Trees
Unrooted Trees
Split Graphs
Finding the
k
Best Phylogenetic Trees
Generating Random Phylogenetic Trees
Multiple Sequence Alignments
Probabilistic Ancestral Sequences
Predicting Secondary Structure
Random Sequence Generation
Searching with Fragment Sequences
Generating random scores
Computing expected scores
Molecular Weight Traces
The comparison algorithm
Probability foundations
Example and probability estimates
The Reference Guide
Programming Tools and Functions
Sets, Lists, Arrays and Strings
Searching Functions
Graphic Functions
Statistical Functions
Randomization Functions
Mathematical Functions
Printing Routines
Input and Output Functions
Nucleic, Amino Acid and Genetic Code Functions
Nucleic Acids
Amino Acids
Standard Genetic Code
Dayhoff and Mutation Matrix Functions
Nucleic Peptide Matching Functions
Pairwise Matching Functions
Backwards Dynamic Programming
Dynamic Programming
All against All Functions
Graph and Tree Functions
Tree Construction Functions
Multiple Sequence Alignment and Probabilistic Ancestral Sequence Functions
Secondary Structure Prediction Functions
Enzyme Digestion Functions
System Functions and Variables
HTML Functions
Interprocessor Functions
External Function Call Functions
Types, Operators and Expressions
Simple Data Types
Relational and Logical Operators
The Order of Operations
Error Messages
The Appendices
Installation Instructions
Naming Conventions
Built-in Types
Structured Types
Commands
Built-In Functions
Library Functions
Name Conversion List
Scripts for Updating Code
Bibliography
Gaston Gonnet
1998-09-15