|
CMAPLE 1
CMaple phylogenetic software
|
#include <tools.h>
Program parameters, everything is specified here
| std::string cmaple::Params::aln_path |
Path to input sequences
| std::string cmaple::Params::ref_path |
Name of an alignment that contains the reference sequence
| std::string cmaple::Params::ref_seqname |
Name of the reference sequence
| std::string cmaple::Params::aln_format_str |
Alignment format
| std::string cmaple::Params::sub_model_str |
Substitution model (e.g., HKY, GTR, JC, etc.)
| bool cmaple::Params::overwrite_output |
TRUE to override the output files
| bool cmaple::Params::fixed_blengths |
TRUE to fixed the branch lengths in the input tree
| RealNumType cmaple::Params::threshold_prob |
A relative probability threshold, which is used to ignore possible states with very low probabilities. Default: 1e-8
| RealNumType cmaple::Params::threshold_prob2 |
threshold_prob ^ 2
| int cmaple::Params::failure_limit_sample |
The number to limit the attempts of seeking a placement for a sample
| int cmaple::Params::failure_limit_subtree |
The number to limit the attempts of seeking a placement for a subtree
| int cmaple::Params::failure_limit_subtree_short_search |
The number to limit the attempts of seeking a placement for a subtree (short range search)
| bool cmaple::Params::strict_stop_seeking_placement_sample |
TRUE to apply strict stop rules when seeking placement for a new
sample
| bool cmaple::Params::strict_stop_seeking_placement_subtree |
TRUE to apply strict stop rules when seeking placement for a subtree
| bool cmaple::Params::strict_stop_seeking_placement_subtree_short_search |
TRUE to apply strict stop rules when seeking placement for a subtree
(short range search)
| RealNumType cmaple::Params::thresh_log_lh_sample |
Threshold of loglh to continue explore the subtree to seek a placement for a sample
| RealNumType cmaple::Params::thresh_log_lh_subtree |
Threshold of loglh to continue explore the subtree to seek a placement for a subtree
| RealNumType cmaple::Params::thresh_log_lh_subtree_short_search |
Threshold of loglh to continue explore the subtree to seek a placement for a subtree (short range search)
| RealNumType cmaple::Params::thresh_log_lh_failure |
Threshold of loglh to count failure
| RealNumType cmaple::Params::fixed_min_blength |
A minimum value of the branch lengths. Default: -1 (UNSPECIFIED), the minimum branch length is computed from 'min_blength_factor'
| RealNumType cmaple::Params::min_blength_factor |
A factor to compute the minimum branch length (if fixed_min_blength is specified, this factor is ignored). Default: 0.2
<Minimum branch length> = <min_blength_factor> * <default branch length>
where <default branch length> is one mutation per site.
| RealNumType cmaple::Params::max_blength_factor |
A factor to compute the maximum branch length. Default: 40
<Maximum branch length> = <max_blength_factor> * <default branch length>
where <default branch length> is one mutation per site.
| RealNumType cmaple::Params::min_blength_mid_factor |
The minium branch length (for mid-branch point) to try for placement
| RealNumType cmaple::Params::thresh_diff_update |
Threshold to determine whether a changed partial is different from its former value
| RealNumType cmaple::Params::thresh_diff_fold_update |
Threshold to determine whether a changed partial is different from its former value by folds
| PositionType cmaple::Params::mutation_update_period |
The period (in term of the number of sample placements) to update the substitution rate matrix. Default: 25
| std::string cmaple::Params::output_aln |
Name of the output alignment
| std::string cmaple::Params::output_aln_format_str |
Format of the output alignment
| std::string cmaple::Params::input_treefile |
Path to an input tree
| int32_t cmaple::Params::num_tree_improvement |
The number of times we traverse the tree looking for topological improvements (applying SPR moves). Default: 1
| RealNumType cmaple::Params::thresh_placement_cost |
Do not try to apply SPR moves on nodes that have the placement cost (i.e. the likelihood contribution by placing a node on the tree) exceeds this threshold. Default: -1e-5
| RealNumType cmaple::Params::thresh_entire_tree_improvement |
Threshold to stop the tree search. If the total log likelihood improvement obtained by an iteration of tree search is lower than this threshold, CMaple stops doing tree search . Default: 1
| RealNumType cmaple::Params::thresh_placement_cost_short_search |
Don't try to re-place nodes (during short range topology search) that have the placement cost exceeds this threshold
| std::string cmaple::Params::tree_format_str |
format of the output tree
| bool cmaple::Params::shallow_tree_search |
TRUE to run an additional short range search for tree topology improvement
| char* cmaple::Params::output_testing |
path to output testing codes
| bool cmaple::Params::compute_aLRT_SH |
TRUE to compute aLRT-SH
| PositionType cmaple::Params::aLRT_SH_replicates |
Number of replicates to compute aLRT-SH
| RealNumType cmaple::Params::aLRT_SH_half_epsilon |
(Half) epsilon value when computing aLRT-SH
| uint32_t cmaple::Params::num_threads |
number of threads
| uint64_t cmaple::Params::ran_seed |
A seed number for random generators. Default: the clock of the PC. Be careful! To make the results reproducible, users should specify the seed number.
| std::string cmaple::Params::output_prefix |
prefix output
| bool cmaple::Params::allow_replace_input_tree |
TRUE to allow replace the input tree by its NNI neighbor (with a higher lh) when computing aLRT-SH
| std::string cmaple::Params::seq_type_str |
type of sequences
| std::string cmaple::Params::tree_search_type_str |
type of tree search
| bool cmaple::Params::make_consistent |
TRUE to make the processes of outputting->re-inputting a tree consistent
1.9.8