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main.c
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main.c
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/***
* Created: unknown
* Author: liheng
* Last MDF: 2005-01-13
*
*
* 2005-01-13 liheng:
*
* * add merge component
*/
#include <string.h>
#include <stdlib.h>
#ifndef _WIN32
#include <unistd.h>
#endif
#include <time.h>
#include "tree.h"
#include "phyml.h"
int tr_sdi_task(int argc, char *argv[]);
int tr_build(int argc, char *argv[]);
int tr_root_task(int argc, char *argv[]);
int tr_reformat_task(int argc, char *argv[]);
int tr_filter_task(int argc, char *argv[]);
int tr_trans_task(int argc, char *argv[]);
int tr_treedist_task(int argc, char *argv[]);
int tr_leaf_task(int argc, char *argv[]);
int tr_mfa2aln_task(int argc, char *argv[]);
int tr_ortho_task(int argc, char *argv[]);
int tr_distmat_task(int argc, char *argv[]);
int tr_mmerge_task(int argc, char *argv[]);
int pwalign_task(int argc, char *argv[]);
int tr_subtree_task(int argc, char *argv[]);
int tr_simulate_task(int argc, char *argv[]);
int tr_sortleaf_task(int argc, char *argv[]);
int tr_estlen_task(int argc, char *argv[]);
int best_task(int argc, char *argv[]);
int plot_eps_task(int argc, char *argv[]);
int ma_backtrans_task(int argc, char *argv[]);
int tr_trimpoor_task(int argc, char *argv[]);
void usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: TreeBeST (gene Tree Building guided by Species Tree)\n");
fprintf(stderr, "Version: %s build %s\n", TR_VERSION, TR_BUILD);
fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
fprintf(stderr, "Usage: treebest <command> [options]\n\n");
fprintf(stderr, "Command: nj build neighbour-joining tree, SDI, rooting\n");
fprintf(stderr, " best build tree with the help of a species tree\n");
fprintf(stderr, " phyml build phyml tree\n");
fprintf(stderr, " sdi speciation vs. duplication inference\n");
fprintf(stderr, " spec print species tree\n");
fprintf(stderr, " format reformat a tree\n");
fprintf(stderr, " filter filter a multi-alignment\n");
fprintf(stderr, " trans translate coding nucleotide alignment\n");
fprintf(stderr, " backtrans translate aa alignment back to nt\n");
fprintf(stderr, " leaf get external nodes\n");
fprintf(stderr, " mfa2aln convert MFA to ALN format\n");
fprintf(stderr, " ortho ortholog/paralog inference\n");
fprintf(stderr, " distmat distance matrix\n");
fprintf(stderr, " treedist topological distance between two trees\n");
fprintf(stderr, " pwalign pairwise alignment\n");
fprintf(stderr, " mmerge merge a forest\n");
fprintf(stderr, " export export a tree to EPS format\n");
fprintf(stderr, " subtree extract the subtree\n");
fprintf(stderr, " simulate simulate a gene tree\n");
fprintf(stderr, " sortleaf sort leaf order\n");
fprintf(stderr, " estlen estimate branch length\n");
fprintf(stderr, " trimpoor trim out leaves that affect the quality of a tree\n");
fprintf(stderr, " root root a tree by minimizing height\n\n");
}
int main(int argc, char *argv[])
{
#ifdef _WIN32
srand(time(0));
#else
srand48(time(0)^((int)getpid()));
#endif
if (argc == 1) {
usage();
return 1;
}
if (strcmp(argv[1], "nj") == 0)
return tr_build(argc-1, argv+1);
else if (strcmp(argv[1], "best") == 0)
return best_task(argc-1, argv+1);
else if (strcmp(argv[1], "phyml") == 0)
return phyml_task(argc-1, argv+1);
else if (strcmp(argv[1], "sdi") == 0)
return tr_sdi_task(argc-1, argv+1);
else if (strcmp(argv[1], "root") == 0)
return tr_root_task(argc-1, argv+1);
else if (strcmp(argv[1], "format") == 0)
return tr_reformat_task(argc-1, argv+1);
else if (strcmp(argv[1], "filter") == 0)
return tr_filter_task(argc-1, argv+1);
else if (strcmp(argv[1], "trans") == 0)
return tr_trans_task(argc-1, argv+1);
else if (strcmp(argv[1], "backtrans") == 0)
return ma_backtrans_task(argc-1, argv+1);
else if (strcmp(argv[1], "leaf") == 0)
return tr_leaf_task(argc-1, argv+1);
else if (strcmp(argv[1], "treedist") == 0)
return tr_treedist_task(argc-1, argv+1);
else if (strcmp(argv[1], "mfa2aln") == 0)
return tr_mfa2aln_task(argc-1, argv+1);
else if (strcmp(argv[1], "ortho") == 0)
return tr_ortho_task(argc-1, argv+1);
else if (strcmp(argv[1], "distmat") == 0)
return tr_distmat_task(argc-1, argv+1);
else if (strcmp(argv[1], "pwalign") == 0)
return pwalign_task(argc-1, argv+1);
else if (strcmp(argv[1], "mmerge") == 0)
return tr_mmerge_task(argc-1, argv+1);
else if (strcmp(argv[1], "export") == 0)
return plot_eps_task(argc-1, argv+1);
else if (strcmp(argv[1], "subtree") == 0)
return tr_subtree_task(argc-1, argv+1);
else if (strcmp(argv[1], "simulate") == 0)
return tr_simulate_task(argc-1, argv+1);
else if (strcmp(argv[1], "sortleaf") == 0)
return tr_sortleaf_task(argc-1, argv+1);
else if (strcmp(argv[1], "estlen") == 0)
return tr_estlen_task(argc-1, argv+1);
else if (strcmp(argv[1], "trimpoor") == 0)
return tr_trimpoor_task(argc-1, argv+1);
else if (strcmp(argv[1], "spec") == 0) {
extern char *tr_species_tree_string;
printf("%s\n", tr_species_tree_string);
return 0;
} else {
fprintf(stderr, "[main] unrecognized command %s\n", argv[1]);
return 1;
}
return 0;
}