Maximum likelihood CLI

treeflow_ml

Perform fixed-topology maximum likelihood inference for a phylogenetic model with a given tree topology and multiple sequence alignment.

The tree prior and substitution model used can be specified using the TreeFlow YAML model definition format (see the package documentation).

Usage

treeflow_ml [OPTIONS]

Options

-i, --input <input>

Required Alignment file (FASTA format)

-t, --topology <topology>

Required Topology file

-m, --model-file <model_file>

YAML model definition file

-n, --num-steps <num_steps>

Required Number of VI iterations

-o, --optimizer <optimizer>

Required

Options:

adam | robust_adam

-r, --learning-rate <learning_rate>

Required

--init-values <init_values>

--alignment-format <alignment_format>

Required File format for alignment

Default:

'fasta'

Options:

fasta | nexus | nexml | phylip

--subnewick-format <subnewick_format>

Required Subnewick format (see ete3.Tree)

Default:

0

--trace-output <trace_output>

--variables-output <variables_output>

--tree-output <tree_output>

--progress-bar, --no-progress-bar