AITEC Contract Research Projects in FY1995 : Software

(16) Application of Parallel Logic Programming for Reconstruction of Molecular Phylogenetic Trees using the Maximum Likelihood Method

Dr. Susumu Kunifuji, Professor, Japan Advanced Institute of Science and Technology

The molecular evolution inference software


by

Satoshi OOta
at
Department of Genetics,
School of Life Science,
The Graduate University of Advanced Studies
at
Laboratory of Evolutionary Genetics,
National Institute of Genetics



[Features of the Software]

`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 a sequence data set intelligently, and infers a reliable molecular phylogenetic tree.

`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 include useful predicates, and users can construct new customized programs easily in the scheme of logic programming.

[Required Environment]

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

[File Configuration]

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 a 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
----------------------------------------------------------------------------

[Others]

This version is a prototype of `DeepForest'. User can use only some of the functions of `DeepForest', and I should warn you that the present version is extremely slow. Almost all the programs are written using KL1, and can be compiled by klic.

[FTP]



www-admin@icot.or.jp