GeneDoc's Purpose and Features.

GeneDoc is a full featured Multiple Sequence Alignment Editor
and Shading Utility. GeneDoc is also intended to help you bring 
your genetics research work to publication with lots of shading, 
page and font layout features. This is a utility that reads either 
.MSF Multiple Sequence alignment files or can Import Fasta Format
files to be saved as a .MSF file project.

GeneDoc is an alignment editor, that is it allows you to Edit the 
Alignment so that different residues from each sequence are lined 
up with each other. This is accomplished by moving the residues in 
one (or all but one) sequence relative to the other sequences by 
inserting or deleting gaps. GeneDoc also features the exclusive 
Grab and Drag mode, arranging residues like beads on a string. A 
residue editing mode is available to allow you to change the 
residues values themselves. Built in DayHoff and BlockSum scoring 
functions allow you to be sure your alignment changes are 
improving the score. Scores can be determined either by a Sum of 
Pairs method or with the Phylogenetic tree support. GUI 
implimentation makes it all so easy to use!

GeneDoc also provides a comprehensive range of Display Shading 
Modes, functions and capabilities. Outlined below, these functions 
give flexible ways to look at the data and to show important 
concepts. Shading can even be done manually!

GeneDoc provides output many different ways. You can print 
directly to the printer, export BitMaps, Text or MAC style Pict 
files.

GeneDoc's features include:

Four different display modes which help focus attention on 
different important aspects of multiple sequence alignments.

     Conservation mode focuses attention on residues that must 
remain constant or nearly so to maintain the functional and 
structural integrity of the molecule. 
     Differences mode focuses attention on variable regions in the 
sequence which can be important in adapting to new environments or 
the evolution of a new function. 
     Quantify mode focuses attention on the pattern of changes in 
different variable positions. This provides an indication of the 
consistency with which different positions in the sequence reflect 
the same evolutionary history. 
     Properties mode focuses attention on residues that have 
maintained a specific chemical or physical property throughout the 
evolution of the molecule even though the specific residue varies. 


Scoring function allows quantitative evaluation of whether 
alignment changes are improving or degrading the alignment.

Score with either Sum of Pairs or with Phylogenetic Trees.

Import Phylogentic trees in either Phylipis or Nexus formats, or 
build your own with GeneDoc's GUI interface.

Widely used similarity scores for both proteins and nucleic acids 
are built in.

Calculation and display of consensus sequences. 

Objective definitions of what substitutions are conservative based 
on positive scores in amino acid and nucleotide similarity tables.

The user can define groups of residues to be treated as equivalent 
for highlighting purposes.

The statistics function summarizes the similarity and divergence 
among the pairs of sequences.

Complete user control of highlighting. 

     Up to three user definable levels that can be applied automatically. 
     Manual highlighting (or removal of highlighting) at the 
individual residue level. 
     Highlighting in either color or gray scale. 

Subsections of an alignment illustrating specific or special 
points can be easily created and saved independently without 
disturbing the main alignment.

Annotation can be added, by the user, either above or below the 
alignment.

Sequences can easily be added, deleted or reordered within the 
alignment.

Uses the widely used Genetics Computer Group (GCG) .msf multiple 
sequence file format for convenient import and export of 
alignments.

Flexible page layout for printing and publication as well as 
control of the font, the font size, and other font attributes.

Copy function to put highlighted and annotated alignments into 
word processing programs or presentation programs as BitMaps, Text 
Files or Pict Files.

Residue Editing Mode to easy modification of data.