micca-phylogenyΒΆ

performs a multiple (denovo o template) alignment and builds the phylogenetic tree.

$ micca-phylogeny --help
usage: micca-phylogeny [-h] [-v] [-a {denovo_muscle,denovo_tcoffe,template}]
                       [-f] [-m {jc,gtr}] [-t {newick,phyloxml,nexus}]
                       [-o DIR] [--muscle-fast] [--tcoffe-num-threads NUM]
                       [--template-file FILE] [--template-min-perc PERC]
                       [--template-min-len LEN]
                       input

micca-phylogeny performs a multiple (denovo o template) alignment and builds the
phylogenetic tree.

positional arguments:
  input                 input fasta file

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -a {denovo_muscle,denovo_tcoffe,template}, --alignment {denovo_muscle,denovo_tcoffe,template}
                        multiple alignment method (default denovo_muscle)
  -f, --tree-fast       speed up the neighbor joining phase and reduce memory
                        usage (recommended for >50,000 sequences)
  -m {jc,gtr}, --tree-model {jc,gtr}
                        tree model: Jukes-Cantor ('jc') or generalized time-
                        reversible ('gtr') (default jc)
  -t {newick,phyloxml,nexus}, --tree-format {newick,phyloxml,nexus}
                        tree format (default newick)
  -o DIR, --output-dir DIR
                        output directory (default .)

Muscle alignment:
  --muscle-fast         a good compromise between speed and accuracy

T-Coffe alignment:
  --tcoffe-num-threads NUM
                        number of threads to use in T-Coffe (default 1)

Template alignment:
  --template-file FILE  template fasta file
  --template-min-perc PERC
                        minimum percent sequence identity to consider a
                        sequence a match (default 75)
  --template-min-len LEN
                        minimum sequence length to include in alignment
                        (default 100)

Example:

 $ micca-phylogeny input.fasta -a template --template-file template.fasta \
   -o phylo

micca v. 0.1.
Author: Davide Albanese <davide.albanese@fmach.it>
Fondazione Edmund Mach, 2014.

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