Enumerate all main functions in IQtree2

[khiron]

Collect functions from the main module that need to be implemented in a shared library version of IQTREE2

[khiron]

General options applicable to most functions

• s:str (Alignment files or directory)
• seqtype:str (Sequence type (BIN, DNA, AA, NT2AA, CODON, MORPH))
• t:str (Starting tree)
• o:str (Outgroup taxon)
• prefix:str (Prefix for output files)
• seed:int (Random seed)
• safe:bool (Safe mode)
• mem:int (Maximum memory usage (MB))
• runs:int (Number of independent runs)
• verbose:bool (Verbose mode)
• version:bool (Show version and exit)
• quiet:bool (Quiet mode)
• fconst:str (Fixed base frequencies)
• epsilon:float (Log-likelihood epsilon)
• T:int (Number of threads)
• threads-max:int (Maximum number of threads)

[khiron]

Phylogenetic Analysis

• aln_file: str (path to the alignment file)
• partition_file: str (path to the partition file)
• tree_file: str (path to the initial tree file)
• out_prefix: str (prefix for output files)
• num_threads: int (number of threads to use)
• seed: int (random seed)

[khiron]

Random Tree Generation

• num_taxa: int (number of taxa for the random tree)
• branch_length_mode: str (mode for generating branch lengths)

Parsimony Multistate

• input_file: str (path to the input file containing multistate data)

RF Distance Calculation

• tree1_file: str (path to the first tree file)
• tree2_file: str (path to the second tree file)

Input File Testing

• input_file: str (path to the input file to be tested)

Print Taxa

• tree_file: str (path to the tree file)

Print Area

• tree_file: str (path to the tree file)

Scale Branch Length

• tree_file: str (path to the tree file)
• scale_factor: float (factor to scale the branch lengths)

PD Distribution

• tree_file: str (path to the tree file)
• taxa_set_file: str (path to the file containing taxa sets)

Branch Statistics

• tree_file: str (path to the tree file)

Tree Clustering

• tree_file: str (path to the tree file)
• cluster_threshold: float (threshold for clustering)

NCBI Tree Processing

• ncbi_taxid_file: str (path to the file containing NCBI taxid)

ECO PD Analysis

• tree_file: str (path to the tree file)
• eco_dag_file: str (path to the ECO DAG file)

All NNI Trees

• tree_file: str (path to the tree file)

Guided Bootstrap

• tree_file: str (path to the tree file)
• siteLL_file: str (path to the site log-likelihood file)

Multiple Probabilities Calculation

• tree_file: str (path to the tree file)
• second_align_file: str (path to the second alignment file)