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version 2.0-rc (release candidate)
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@bqminh
bqminh committed Nov 19, 2019
1 parent 5888793 commit 377ab66
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6 changes: 3 additions & 3 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -79,9 +79,9 @@ endif()


# The version number.
set (iqtree_VERSION_MAJOR 1)
set (iqtree_VERSION_MINOR 7)
set (iqtree_VERSION_PATCH "-beta18")
set (iqtree_VERSION_MAJOR 2)
set (iqtree_VERSION_MINOR 0)
set (iqtree_VERSION_PATCH "-rc")

option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)

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5 changes: 1 addition & 4 deletions main/phyloanalysis.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -879,9 +879,6 @@ void printOutfilesInfo(Params &params, IQTree &tree) {
/* if (params.model_name == "WHTEST")
cout <<" WH-TEST report: " << params.out_prefix << ".whtest" << endl;*/

if (params.terrace_analysis)
cout << " Terrace trees written to: " << params.out_prefix << ".terrace" << endl;

cout << endl;

}
Expand Down Expand Up @@ -1263,7 +1260,7 @@ void reportPhyloAnalysis(Params &params, IQTree &tree, ModelCheckpoint &model_in
}
#ifdef IQTREE_TERRAPHAST
if (params.terrace_analysis) {
out << "TERRACE ANALYSIS" << endl << "--------------" << endl << endl;
out << "TERRACE ANALYSIS" << endl << "----------------" << endl << endl;

string filename = params.out_prefix;
filename += ".terrace";
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91 changes: 51 additions & 40 deletions utils/tools.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -860,7 +860,11 @@ void parseArg(int argc, char *argv[], Params &params) {
params.partfinder_log_rate = true;
params.remove_empty_seq = true;
params.terrace_aware = true;
#ifdef IQTREE_TERRAPHAST
params.terrace_analysis = true;
#else
params.terrace_analysis = false;
#endif
params.sequence_type = NULL;
params.aln_output = NULL;
params.aln_site_list = NULL;
Expand Down Expand Up @@ -1137,7 +1141,7 @@ void parseArg(int argc, char *argv[], Params &params) {
#endif
continue;
}
if (strcmp(argv[cnt], "-version") == 0 || strcmp(argv[cnt], "--version") == 0) {
if (strcmp(argv[cnt], "-V") == 0 || strcmp(argv[cnt], "-version") == 0 || strcmp(argv[cnt], "--version") == 0) {
printCopyright(cout);
exit(EXIT_SUCCESS);
}
Expand Down Expand Up @@ -2085,7 +2089,13 @@ void parseArg(int argc, char *argv[], Params &params) {
#endif
continue;
}
if (strcmp(argv[cnt], "-sf") == 0) {

if (strcmp(argv[cnt], "--no-terrace") == 0) {
params.terrace_analysis = false;
continue;
}

if (strcmp(argv[cnt], "-sf") == 0) {
cnt++;
if (cnt >= argc)
throw "Use -sf <ngs_file>";
Expand Down Expand Up @@ -2731,13 +2741,15 @@ void parseArg(int argc, char *argv[], Params &params) {
throw "Wrong number of threads";
continue;
}
if (strcmp(argv[cnt], "-b") == 0 || strcmp(argv[cnt], "-j") == 0 || strcmp(argv[cnt], "-bo") == 0 || strcmp(argv[cnt], "--bonly") == 0) {
if (strcmp(argv[cnt], "-b") == 0 || strcmp(argv[cnt], "--boot") == 0 ||
strcmp(argv[cnt], "-j") == 0 || strcmp(argv[cnt], "--jack") == 0 ||
strcmp(argv[cnt], "-bo") == 0 || strcmp(argv[cnt], "--bonly") == 0) {
params.multi_tree = true;
if (strcmp(argv[cnt], "-bo") == 0 || strcmp(argv[cnt], "--bonly") == 0)
params.compute_ml_tree = false;
else
params.consensus_type = CT_CONSENSUS_TREE;
if (strcmp(argv[cnt], "-j") == 0 && params.jackknife_prop == 0.0)
if ((strcmp(argv[cnt], "-j") == 0 || strcmp(argv[cnt], "--jack") == 0) && params.jackknife_prop == 0.0)
params.jackknife_prop = 0.5;
cnt++;
if (cnt >= argc)
Expand All @@ -2751,7 +2763,7 @@ void parseArg(int argc, char *argv[], Params &params) {
params.consensus_type = CT_NONE;
continue;
}
if (strcmp(argv[cnt], "--bsam") == 0 || strcmp(argv[cnt], "-bsam") == 0) {
if (strcmp(argv[cnt], "--bsam") == 0 || strcmp(argv[cnt], "-bsam") == 0 || strcmp(argv[cnt], "--sampling") == 0) {
cnt++;
if (cnt >= argc)
throw "Use -bsam <bootstrap_specification>";
Expand Down Expand Up @@ -2813,7 +2825,7 @@ void parseArg(int argc, char *argv[], Params &params) {
continue;
}

if (strcmp(argv[cnt], "-wt") == 0) {
if (strcmp(argv[cnt], "-wt") == 0 || strcmp(argv[cnt], "--treels") == 0) {
params.write_intermediate_trees = 1;
continue;
}
Expand Down Expand Up @@ -2940,12 +2952,12 @@ void parseArg(int argc, char *argv[], Params &params) {
throw "Local bootstrap (LBP) replicates must be at least 1000";
continue;
}
if (strcmp(argv[cnt], "-wsl") == 0) {
if (strcmp(argv[cnt], "-wsl") == 0 || strcmp(argv[cnt], "--sitelh") == 0) {
params.print_site_lh = WSL_SITE;
continue;
}

if (strcmp(argv[cnt], "-wpl") == 0) {
if (strcmp(argv[cnt], "-wpl") == 0 || strcmp(argv[cnt], "--partlh") == 0) {
params.print_partition_lh = true;
continue;
}
Expand Down Expand Up @@ -3204,12 +3216,13 @@ void parseArg(int argc, char *argv[], Params &params) {
params.eco_run = convert_int(argv[cnt]);
continue;
}
if (strcmp(argv[cnt], "-bb") == 0 || strcmp(argv[cnt], "-B") == 0 || strcmp(argv[cnt], "-J") == 0) {
if (strcmp(argv[cnt], "-J") == 0 && params.jackknife_prop == 0.0)
if (strcmp(argv[cnt], "-bb") == 0 || strcmp(argv[cnt], "-B") == 0 || strcmp(argv[cnt], "--ufboot") == 0 ||
strcmp(argv[cnt], "-J") == 0 || strcmp(argv[cnt], "--ufjack") == 0) {
if ((strcmp(argv[cnt], "-J") == 0 || strcmp(argv[cnt], "--ufjack") == 0) && params.jackknife_prop == 0.0)
params.jackknife_prop = 0.5;
cnt++;
if (cnt >= argc)
throw "Use -bb <#replicates>";
throw "Use -B <#replicates>";
if (params.stop_condition == SC_FIXED_ITERATION) {
throw("Ultrafast bootstrap does not work with -fast, -te or -n option");
}
Expand All @@ -3231,7 +3244,7 @@ void parseArg(int argc, char *argv[], Params &params) {
throw "Epsilon must be positive";
continue;
}
if (strcmp(argv[cnt], "-wbt") == 0 || strcmp(argv[cnt], "--wbt") == 0) {
if (strcmp(argv[cnt], "-wbt") == 0 || strcmp(argv[cnt], "--wbt") == 0 || strcmp(argv[cnt], "--boot-trees") == 0) {
params.print_ufboot_trees = 1;
continue;
}
Expand Down Expand Up @@ -3535,7 +3548,7 @@ void parseArg(int argc, char *argv[], Params &params) {
params.pll = true;
continue;
}
if (strcmp(argv[cnt], "-me") == 0 || strcmp(argv[cnt], "--model-epsilon") == 0) {
if (strcmp(argv[cnt], "-me") == 0 || strcmp(argv[cnt], "--epsilon") == 0) {
cnt++;
if (cnt >= argc)
throw "Use -me <model_epsilon>";
Expand Down Expand Up @@ -3961,7 +3974,7 @@ void parseArg(int argc, char *argv[], Params &params) {
continue;
}

if (strcmp(argv[cnt], "--force-unfinish") == 0) {
if (strcmp(argv[cnt], "--undo") == 0) {
params.force_unfinished = true;
continue;
}
Expand Down Expand Up @@ -4211,20 +4224,26 @@ void usage_iqtree(char* argv[], bool full_command) {
printCopyright(cout);
cout << "Usage: iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ..." << endl << endl;
cout << "GENERAL OPTIONS:" << endl
<< " -h Print this help dialog" << endl
<< " --help Print more available options" << endl
<< " --version Display version number" << endl
<< " -s FILE PHYLIP/FASTA/NEXUS/CLUSTAL/MSF sequence alignment" << endl
<< " -h, --help Print (more) help usages" << endl
<< " -s FILE[,...,FILE] PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)" << endl
<< " -s DIR Directory of alignment files" << endl
<< " --seqtype STRING BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)" << endl
<< " -t FILE|PARS|RAND Starting tree (default: 99 parsimony and BIONJ)" << endl
<< " --tree-fix Fix -t tree (no tree search performed)" << endl
<< " -o TAX[,...,TAX] Outgroup taxon (list) for writing .treefile" << endl
<< " --prefix STRING Prefix for all output files (default: aln/partition)" << endl
<< " --seed NUMBER Random seed number, normally used for debugging purpose" << endl
<< " --safe Safe likelihood kernel to avoid numerical underflow" << endl
<< " --mem NUMBER[G|M|%] Maximal RAM usage in GB | MB | %" << endl
<< " --runs NUMBER Number of indepedent runs (default: 1)" << endl
<< " --redo Ignore checkpoint and overwrite outputs (default: OFF)" << endl
<< " -v, --verbose Verbose mode, printing more messages to screen" << endl
<< " -V, --version Display version number" << endl
<< " --quiet Quiet mode, suppress printing to screen (stdout)" << endl
<< " -fconst f1,...,fN Add constant patterns into alignment (N=no. states)" << endl
<< " --epsilon NUMBER Likelihood epsilon for parameter estimate (default 0.01)" << endl
#ifdef _OPENMP
<< " -T NUMBER|AUTO No. cores/threads or AUTO-detect (default: 1)" << endl
<< " --threads-max NUM Max number of threads for -T AUTO (default: all cores)" << endl
#endif
<< endl << "PARTITION MODEL:" << endl
<< " -p FILE|DIR NEXUS/RAxML partition file or directory with alignments" << endl
Expand All @@ -4249,27 +4268,30 @@ void usage_iqtree(char* argv[], bool full_command) {
<< " -g FILE (Multifurcating) topological constraint tree file" << endl
<< " --fast Fast search to resemble FastTree" << endl
<< " --polytomy Collapse near-zero branches into polytomy" << endl
<< " --tree-fix Fix -t tree (no tree search performed)" << endl
<< " --treels Write locally optimal trees into .treels file" << endl
<< " --show-lh Compute tree likelihood without optimisation" << endl
#ifdef IQTREE_TERRAPHAST
<< " --terrace Check if the tree lies on a phylogenetic terrace" << endl
#endif
// << " -iqp Use the IQP tree perturbation (default: randomized NNI)" << endl
// << " -iqpnni Switch back to the old IQPNNI tree search algorithm" << endl
<< endl << "ULTRAFAST BOOTSTRAP/JACKKNIFE:" << endl
<< " -B NUMBER Replicates for ultrafast bootstrap (>=1000)" << endl
<< " -J NUMBER Replicates for ultrafast jackknife (>=1000)" << endl
<< " -B, --ufboot NUMBER Replicates for ultrafast bootstrap (>=1000)" << endl
<< " -J, --ufjack NUMBER Replicates for ultrafast jackknife (>=1000)" << endl
<< " --jack-prop NUMBER Subsampling proportion for jackknife (default: 0.5)" << endl
<< " --bsam STRING GENE|GENESITE resampling for partitions (default: SITE)" << endl
<< " --wbt Write bootstrap trees to .ufboot file (default: none)" << endl
<< " --wbtl Like -wbt but also writing branch lengths" << endl
<< " --sampling STRING GENE|GENESITE resampling for partitions (default: SITE)" << endl
<< " --boot-trees Write bootstrap trees to .ufboot file (default: none)" << endl
<< " --wbtl Like --boot-trees but also writing branch lengths" << endl
// << " -n <#iterations> Minimum number of iterations (default: 100)" << endl
<< " --nmax NUMBER Maximum number of iterations (default: 1000)" << endl
<< " --nstep NUMBER Iterations for UFBoot stopping rule (default: 100)" << endl
<< " --bcor NUMBER Minimum correlation coefficient (default: 0.99)" << endl
<< " --beps NUMBER RELL epsilon to break tie (default: 0.5)" << endl
<< " --bnni Optimize UFBoot trees by NNI on bootstrap alignment" << endl
<< endl << "NON-PARAMETRIC BOOTSTRAP/JACKKNIFE:" << endl
<< " -b NUMBER Replicates for bootstrap + ML tree + consensus tree" << endl
<< " -j NUMBER Replicates for jackknife + ML tree + consensus tree" << endl
<< " -b, --boot NUMBER Replicates for bootstrap + ML tree + consensus tree" << endl
<< " -j, --jack NUMBER Replicates for jackknife + ML tree + consensus tree" << endl
<< " --jack-prop NUMBER Subsampling proportion for jackknife (default: 0.5)" << endl
<< " --bcon NUMBER Replicates for bootstrap + consensus tree" << endl
<< " --bonly NUMBER Replicates for bootstrap only" << endl
Expand Down Expand Up @@ -4402,6 +4424,7 @@ void usage_iqtree(char* argv[], bool full_command) {
<< " --test NUMBER Replicates for topology test" << endl
<< " --test-weight Perform weighted KH and SH tests" << endl
<< " --test-au Approximately unbiased (AU) test (Shimodaira 2002)" << endl
<< " --sitelh Write site log-likelihoods to .sitelh file" << endl

<< endl << "ANCESTRAL STATE RECONSTRUCTION:" << endl
<< " --ancestral Ancestral state reconstruction by empirical Bayes" << endl
Expand Down Expand Up @@ -4464,34 +4487,22 @@ void usage_iqtree(char* argv[], bool full_command) {
<< " --rlen NUM NUM NUM min, mean, and max random branch lengths" << endl

<< endl << "MISCELLANEOUS:" << endl
<< " -o STRING Outgroup taxon name for writing .treefile" << endl
<< " --seqtype STRING BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)" << endl
#ifdef _OPENMP
<< " --threads-max NUM Max number of threads for -c AUTO (default: CPU cores)" << endl
#endif
<< " -v, --verbose Verbose mode, printing more messages to screen" << endl
<< " --quiet Quiet mode, suppress printing to screen (stdout)" << endl
<< " --keep-ident Keep identical sequences (default: remove & finally add)" << endl
<< " --cptime NUMBER Checkpoint time interval in seconds (default: 60)" << endl
<< " -wt Write locally optimal trees into .treels file" << endl
<< " -blfix Fix branch lengths of user tree passed via -te" << endl
<< " -blscale Scale branch lengths of user tree passed via -t" << endl
<< " -blmin Min branch length for optimization (default 0.000001)" << endl
<< " -blmax Max branch length for optimization (default 100)" << endl
<< " -wsl Write site log-likelihoods to .sitelh file" << endl
<< " -wslr Write site log-likelihoods per rate category" << endl
<< " -wslm Write site log-likelihoods per mixture class" << endl
<< " -wslmr Write site log-likelihoods per mixture+rate class" << endl
<< " -wspr Write site probabilities per rate category" << endl
<< " -wspm Write site probabilities per mixture class" << endl
<< " -wspmr Write site probabilities per mixture+rate class" << endl
<< " -wpl Write partition log-likelihoods to .partlh file" << endl
<< " -fconst f1,...,fN Add constant patterns into alignment (N=no. states)" << endl
<< " -me NUMBER LogL epsilon for parameter estimation (default 0.01)" << endl
<< " --partlh Write partition log-likelihoods to .partlh file" << endl
<< " --no-outfiles Suppress printing output files" << endl
<< " --eigenlib Use Eigen3 library" << endl
<< " -alninfo Print alignment sites statistics to .alninfo" << endl
<< " --show-lh Compute tree likelihood without optimisation" << endl
// << " -d <file> Reading genetic distances from file (default: JC)" << endl
// << " -d <outfile> Calculate the distance matrix inferred from tree" << endl
// << " -stats <outfile> Output some statistics about branch lengths" << endl
Expand Down Expand Up @@ -4527,7 +4538,7 @@ void quickStartGuide() {
<< "6. Find best partition scheme followed by tree inference and bootstrap:" << endl
<< " iqtree -s example.phy -p example.nex -m MFP+MERGE -B 1000" << endl << endl
#ifdef _OPENMP
<< "7. Use 4 CPU cores to speed up computation: add '-c 4' option" << endl << endl
<< "7. Use 4 CPU cores to speed up computation: add '-T 4' option" << endl << endl
#endif
<< "8. Polymorphism-aware model with HKY nucleotide model and Gamma rate:" << endl
<< " iqtree -s counts_file.cf -m HKY+P+G" << endl << endl
Expand Down

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