Generating Sequences

Basic mode (S)

With this method, it is possible to simulate an alignment (nucleotides, proteins or codons) for each gene that evolve inside the species tree. Sequences are simulated along the branches of the species tree, considering that the branch-length of the gene trees output by the G mode is measured in units of time.

Output

Sequences: A folder with two fasta file per gene of the species tree. each fasta alignment contains the simulated sequences obtained at the leaves of the tree, not the internal nodes.

Parameters

SCALING

Number of substitutions per unit of time

SEQUENCE

codon, amino-acid or nucleotide

VERBOSE

If 1, it inputs the name of the gene family being computed