final static private String INPUT_GENOMES_FILE_OPTION = "genomes";
final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
final static private String SEQ_EXTRACT_OPTION = "prot_extract";
- final static private String PRG_VERSION = "2.502";
- final static private String PRG_DATE = "170511";
+ final static private String PRG_VERSION = "2.503";
+ final static private String PRG_DATE = "170518";
final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing";
final static private boolean IGNORE_DUFS_DEFAULT = true;
ForesterUtil
.programMessage( PRG_NAME,
"Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file );
- final int LEVEL = 2;
+ final int LEVEL = 0;
try {
MinimalDomainomeCalculator.calc( false,
intrees[ 0 ],
.println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" );
System.out.println();
System.out
- .println("[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
+ .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" );
System.out.println();
}
}