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#include <string>
using namespace std;
static string usage() {
string tmp;
tmp +=" |-------------------------------- HELP: -------------------------------------+\n";
tmp +=" | VALUES IN [] ARE DEFAULT VALUES |\n";
tmp +=" |-h help |\n";
tmp +=" |-s sequence input file (for example use -s D:\\mySequences\\seq.txt ) |\n";
tmp +=" |-t tree input file |\n";
tmp +=" | (if tree is not given, a neighbor joining tree is computed). |\n";
tmp +=" |-g Assume among site rate variation model (Gamma) [By default the program |\n";
tmp +=" | will assume an homogeneous model. very fast, but less accurate!] |\n";
tmp += "|-m model name |\n";
tmp += "|-mj [JTT] |\n";
tmp += "|-ml LG |\n";
tmp += "|-mr mtREV (for mitochondrial genomes) |\n";
tmp += "|-md DAY |\n";
tmp += "|-mw WAG |\n";
tmp += "|-mc cpREV (for chloroplasts genomes) |\n";
tmp += "|-ma Jukes and Cantor (JC) for amino acids |\n";
tmp += "|-mn Jukes and Cantor (JC) for nucleotides |\n";
tmp += "|-mh HKY Model for nucleotides |\n";
tmp += "|-mg nucgtr Model for nucleotides |\n";
tmp += "|-mt tamura92 Model for nucleotides |\n";
tmp += "|-my yang M5 codons model |\n";
tmp += "|-me empirical codon matrix |\n";
tmp +=" +----------------------------------------------------------------------------+\n";
tmp +=" |Controling the output options: |\n";
tmp +=" |-x tree file output in Newick format [tree.newick.txt] |\n";
tmp +=" |-y tree file output in ANCESTOR format [tree.ancestor.txt] |\n";
tmp +=" |-j joint sequences output file [seq.joint.txt] |\n";
tmp +=" |-k marginal sequences output file [seq.marginal.txt] |\n";
tmp +=" |-d joint probabilities output file [prob.joint.txt] |\n";
tmp +=" |-e marginal probabilities output file [prob.marginal.txt] |\n";
tmp +=" |-q ancestral sequences output format. -qc = [CLUSTAL], -qf = FASTA |\n";
tmp +=" | -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus |\n";
tmp +=" +----------------------------------------------------------------------------+\n";
tmp +=" |Advances options: |\n";
tmp +=" |-a Threshold for computing again marginal probabilities [0.9] |\n";
tmp +=" |-b Do not optimize branch lengths on starting tree |\n";
tmp +=" | [by default branches and alpha are ML optimized from the data] |\n";
tmp +=" |-c number of discrete Gamma categories for the gamma distribution [8] |\n";
tmp +=" |-f don't compute Joint reconstruction (good if the branch and bound |\n";
tmp +=" | algorithm takes too much time, and the goal is to compute the |\n";
tmp +=" | marginal reconstruction with Gamma). |\n";
tmp +=" |-z The bound used. -zs - bound based on sum. -zm based on max. -zb [both] |\n";
tmp +=" |-p user alpha parameter of the gamma distribution [if alpha is not given, |\n";
tmp +=" | alpha and branches will be evaluated from the data (override -b) |\n";
// tmp +=" |R report file. Show the choices made by the algorithm |\n";
// tmp +=" |-u do not use Chebyshev optimization |\n";
tmp +=" +----------------------------------------------------------------------------+\n";
return tmp;
}
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