treeΒΆ

$ micca tree --help
usage: micca tree [-h] -i FILE -o FILE [-m {fasttree,muscle}] [--fasttree-gtr]
                  [--fasttree-fastest]
                  [--muscle-cluster {upgmb,upgma,neighborjoining}]

micca tree infers phylogenetic trees from alignments. It provides two
methods:

* FastTree (doi: 10.1371/journal.pone.0009490);
* MUSCLE (doi: 10.1093/nar/gkl244).

optional arguments:
  -h, --help            show this help message and exit

arguments:
  -i FILE, --input FILE
                        input FASTA file (required).
  -o FILE, --output FILE
                        output tree in Newick format (required).
  -m {fasttree,muscle}, --method {fasttree,muscle}
                        tree inference method (default fasttree).

FastTree specific options:
  --fasttree-gtr        use the generalized time-reversible (GTR)+CAT model
                        instead of Jukes-Cantor+CAT (default False).
  --fasttree-fastest    speed up the neighbor joining phase and reduce memory
                        usage recommended for >50,000 sequences) (default
                        False).

MUSCLE specific options:
  --muscle-cluster {upgmb,upgma,neighborjoining}
                        clustering algorithm (default upgmb).

Examples

Tree inference using FastTree and the generalized time-reversible
(GTR)+CAT model:

    micca tree -i input.fasta -o tree.tree --fasttree-gtr