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General Index

- A B C D E F G H I L M N O P Q R S T U V W

-

  • --
  • -config
  • -fofn
  • -no_win
  • -nowin
  • -win_compact
  • -win_separate

    • a

  • Adding modules
  • ALF/ABI to SCF conversion configuration
  • ALF/ABI to SCF conversion module
  • Arguments, command line
  • ATQA configuration
  • ATQA module
  • Augment Experiment files configuration
  • Augment Experiment files module
  • Augment, by line types
  • Augment, by text database

    • b

  • Batch mode
  • Blast screen configuration
  • Blast screen module

    • c

  • Cap2 assembly configuration
  • Cap2 assembly module
  • Cap3 assembly configuration
  • Cap3 assembly module
  • Cloning vector clip configuration
  • Cloning vector clip configuration (old style)
  • Cloning vector clip module
  • Cloning vector clip module (old style)
  • Colours
  • Command line arguments
  • Component configuration
  • Components
  • Compress Trace Files configuration
  • Compress Trace Files module
  • Configuration files
  • configuration files: pregap4
  • Configuration: pregap4 low level
  • Configuring modules
  • Configuring pregap4
  • convert_trace
  • Cross_match configuration
  • Cross_match module

    • d

  • Database integration
  • Database, plain text format

    • e

  • Email configuration
  • Email module
  • Enter assembly configuration
  • Enter assembly module
  • Estimate base accuracies configuration
  • Estimate base accuracies module
  • Example code
  • Experiment File line types
  • Extract sequence configuration
  • Extract Sequence module

    • f

  • FakII assembly configuration
  • FakII assembly module
  • FASTA files: pregap4
  • Files, specifying
  • Fonts
  • Functions, builtin
  • Functions, in modules

    • g

  • Gap4 shotgun assembly configuration
  • Gap4 shotgun assembly module
  • General configuration configuration
  • General configuration module
  • Global variables

    • h

  • Heterozygote scanner module

    • i

  • Include config component
  • Information sources
  • Initialise Experiment Files configuration
  • Initialise Experiment files module
  • Interactive clipping configuration
  • Interactive clipping module
  • Introduction

    • l

  • Line types, in experiment file
  • Load naming scheme
  • low level pregap4 configuration

    • m

  • Module functions
  • Module variables
  • Module, example code
  • Modules, adding and removing
  • Modules, configuring
  • Modules, creating
  • Modules, overview
  • Mutation detection configuration
  • Mutation detection module

    • n

  • Naming schemes
  • Naming schemes, creating.
  • naming schemes: mutation detection
  • naming schemes: pregap4
  • Non-interactive processing

    • o

  • Old cloning vector clip configuration

    • p

  • Phrap assembly configuration
  • Phrap assembly module
  • Phred configuration
  • Phred module
  • Pregap4
  • pregap4: FASTA files
  • pregap4: naming schemes
  • pregap4: Reference sequence
  • pregap4: temporary files
  • pregap4rc files

    • q

  • quality clip configuration
  • Quality clip module

    • r

  • Reference sequence: pregap4
  • Reference trace module
  • Removing modules
  • RepeatMasker configuration
  • RepeatMasker module
  • Run command

    • s

  • Sanger Centre naming scheme, new
  • Sanger Centre naming scheme, old
  • Screen for unclipped vector configuration
  • Screen for unclipped vector module
  • Screen sequences configuration
  • Screen sequences module
  • Sequencing vector clip configuration
  • Sequencing vector clip module
  • Shutdown configuration
  • Simple Text Database
  • Styles of windows

    • t

  • Tag repeats configuration
  • Tag repeats module
  • temporary files
  • Trace difference module
  • Trace Format Conversion
  • Trace Format Conversion configuration

    • u

  • Uncalled base clip configuration

    • v

  • Variables, global to all modules
  • Variables, in modules

    • w

  • Window styles

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    This page is maintained by staden-package. Last generated on 22 October 2002.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_unix_94.html