Application programs were provided as shown in table 1.2.
| Name | Description |
| Name | Description |
| check_topology | Computation of topological distances between a model tree and inferred trees |
| sim_3tree | Simulation of evolution and comparison between a model tree and inferred trees using the ThreeTree method with the maximum likelihood correction (for amino acids) |
| sim_3treed | Simulation of evolution and comparison between a model tree and inferred trees using the Distance ThreeTree method (for amino acids) |
| sim_3treen | Simulation of evolution and comparison between a model tree and inferred trees using the ThreeTree method with the maximum likelihood correction (for nucleotides) |
| sim_3treen | Simulation of evolution and comparison between a expected model tree (under the Poisson process) and inferred trees using the ThreeTree method with the maximum likelihood correction (for nucleotides) |
| sim_ml | Simulation of evolution and comparison between a model tree and inferred trees using the exhaustive maximum likelihood method (for nucleotides) |
| sim_nj | Simulation of evolution and comparison between a model tree and inferred trees using the neighbor joining method (for nucleotides) |
| sim_njp | Simulation of evolution and comparison between a expected model tree (under the Poisson process) and inferred trees using the exhaustive maximum likelihood method (for nucleotides) |
| test_tra | Optimization of branch lengths of a given tree in terms of likelihood (for amino acids) |
| make_destbl | Generation of a table for automatic annotation for a phylogenetic tree from a given sequence database |
| make_freq_matrix | Making frequency matrix for a tree of amino acid composition |
| make_gap_matrix | Making gap matrix for a tree of Minimum Gap Matrix tree |
| make_ph | Making phylip format file with annotated data according to a table generated by make_destbl (this program was written in Perl) |
| topology | Output of all possible topologies for a given number of sequences |
| make_records | Making structured file having records from ``flat'' file according to delimiter ``//'' |
| extract_fields | Extraction of indicated fields from a structured file by make_records |
| make_seq | Making a sequence file in FASTA format from a structured file by make_records |
| make_bib | Making bibliography database for BIBTeX [Lamport, 1995] |
| super | Getting the most probable relationship from gene trees by superimposition |