static IntMatrix |
RIO.calculateOrthologTable(Phylogeny[] analyzed_gene_trees,
boolean sort) |
static RIO |
RIO.executeAnalysis(File gene_trees_file,
File species_tree_file,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
int first,
int last,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(File gene_trees_file,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(File gene_trees_file,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
int first,
int last,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(IteratingPhylogenyParser p,
File species_tree_file,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
int first,
int last,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(IteratingPhylogenyParser p,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(IteratingPhylogenyParser p,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
int first,
int last,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(Phylogeny[] gene_trees,
Phylogeny species_tree) |
static RIO |
RIO.executeAnalysis(Phylogeny[] gene_trees,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |
static RIO |
RIO.executeAnalysis(Phylogeny[] gene_trees,
Phylogeny species_tree,
SDIutil.ALGORITHM algorithm,
RIO.REROOTING rerooting,
String outgroup,
int first,
int last,
boolean produce_log,
boolean verbose,
boolean transfer_taxonomy) |