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Application programs

Application programs were provided as shown in table 1.2.

  
Table: Application programs in DeepForest
Table: Application programs in
DeepForest (continued)
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


next up previous
Next: Tree reconstruction Up: Provided predicates and those Previous: Provided predicates
Satoshi OOta
1999-03-06