The molecular evolution inference software

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					### Prototype version (Rev. 0.71) ###
						July 6, 1996

					Copyright (C) 1996 Satoshi OOta

1. What is `DeepForest'?

`DeepForest'  is  a  set  of  predicates   to   infer   molecular
phylogenetic  trees mainly from amino acid sequences. By default,
users can use the maximum likelihood method to infer the   trees.
The   complete  version   of  `DeepForest' analyzes sequence data
set intelligently, and infers a reliable  molecular  phylogenetic
tree.

2. Restriction of the present version

This version is a prototype of `DeepForest'. User can use only  a
part  of  function  on  `DeepForest',  and I should warn you that
the present version is extremely slow. This programs are  written
almost  by KL1, and can be compiled by klic.

3. How to compile `DeepForest'

In directory ./unix, just  make  it.  Of  course,  you  have  to
install the newest version of klic before the compilation.

4. How to run prototype of `DeepForest'

The way to run  the  program  is  quite  simple.  Just  type  the
following command in your shell.

go [Input file name]

The program  begins  to  evaluate  a  given  sequence  data  set.
However, actually, you have to build input data before execution.
Unfortunately, there is no useful utility to make input  file  at
present.  I  have prepared simple-sample input file, by which you
can try to execute `go/0'.  To run 'go/0' using the sample  file,
type  `make  simple' or 'make sample'. I warn you that the latter
data requires extreme long time to terminate (about 66 minutes by
Fujitsu S-4/20L).

5. Parallel execution of `go/0'^*

Parallel   logic   programming   made   `go/0'   executable    in
distributed/parallel  environment.   If distributed/shared memory
klic is available in you  system,  why  don't  you  try  parallel
execution by `go/0'? However, I again warn you, this version does
*not* run efficiently. You  should  not  expect  high-performance
data   analyses.    I   have   tested  distributed `go/0' only on
three clustered workstations.

* We cannot execute 'go/0' correctly in  distributed  environment
using  the  present  version of klic (2.002). Developpers of klic
are trying to fix its bug.

6. Required environment

This prototype version is so small that you can run  `go/0'  even
on   PC   with  the  newest  version  of  klic.  I have tested on
Macintosh (Duo 280c) with Mach Ten. However, complete version  of
`go/0'  will  run  exclusively  on  X  window system.  Also PIMOS
version of `go/0' (contour/1 and traverse/3) is included in  this
file.  Since  these  programs  are  quite  experimental one, only
nucleotide data is available.

7. Concept of `DeepForest'

`DeepForest' is not only  an  application   program,   but   also
set   of  predicates   which   are  useful for data analyses. The
programs  are  presented  as  modules,  which   includes   useful
predicates,  and  users  can   construct  new customized programs
easily in scheme of logic programming.

8. Included files

The following programs are included in this file.

For UNIX
----------------------------------------------------------------------------
name			description
----------------------------------------------------------------------------
calculate.kl1		module for evaluating a symbol as a numerical value
clike.kl1		module evaluating conditional likelihood
get_seq.kl1		gets sequence data 
get_seq_2.kl1		gets sequence data 
go.kl1			go/0 itself
list.kl1		module for list manipulation
max.kl1			selects a symbol having larger numerical value
plot_like.kl1		plots likelihood values
remove_gap_site.kl1	removes gap sites from given sequences
remove_gap_site_2.kl1	removes gap sites from given sequences
string.kl1		module for string manipulation 
symbol.kl1		module for symbol computation
termio.kl1		module for term input/output
traverse.kl1		module for optimizing a tree by traversing branches
tree.kl1		module for tree manipulation
sample.pl		Sample input data
----------------------------------------------------------------------------

For PIMOS
----------------------------------------------------------------------------
name			description
----------------------------------------------------------------------------
contour.kl1		generates a likelihood surface
traverse.kl1		optimizes a tree by traversing branches
----------------------------------------------------------------------------


------------------------------------------------------------
Satoshi OOta (Neither Ota nor Ohta nor Oota, but OOta!)
------------------------------------------------------------
Department of Genetics,
School of Life Science,
The Graduate University of Advanced Studies
at
Laboratory of Evolutionary Genetics,
National Institute of Genetics,
Mishima, 411 Japan
FAX: +81-559-81-6794
TEL: +81-559-81-6790
------------------------------------------------------------

					Copyright (C) 1996 Satoshi OOta

