NAME¶

libpll — Phylogenetic Likelihood Library

SYNOPSIS¶

Partition management

Partition parameters setup

Transition probability matrices

Invariant sites

Conditional probability vectors

Evaluation of log-Likelihood

Likelihood function derivatives

FASTA file handling

PHYLIP file handling

Newick handling

Unrooted tree structure manipulation

Rooted tree structure manipulation

Topological rearrangement moves

Parsimony functions

Auxiliary functions

Core functions

DESCRIPTION¶

libpll is a library for phylogenetics.

pll_partition_t * pll_partition_create(unsigned int tips, unsigned int clv_buffers, unsigned int states, unsigned int sites, unsigned int rate_matrices, unsigned int prob_matrices, unsigned int rate_cats, unsigned int scale_buffers, unsigned int attributes);

Creates a partition with either tips character arrays or tips CLV arrays (depending on attributes, see Partition Attributes), and, additionally, clv_buffers CLV vectors, for storing conditional probabilities at inner nodes. The partition structure is constructed for states number of states (e.g. 4 for nucleotide and 20 for amino-acid data) and sufficient space is allocated to host an alignment of size sites*tips. The number of rate matrices that can be used is given by rate_matrices. Additionally, the function allocates space for hosting rate_matrices arrays of substitution parameters, frequencies, and auxiliary eigen-decomposition arrays (transparent to the user). The parameter prob_matrices dictates the number of probability matrices for which space will be allocated. This parameter is typically set to the number of branches the tree has (e.g., 2n-3 for unrooted and 2n-2 for rooted, where n is the number of tips/leaves). libpll will automatically create space for prob_matrices*rate_cats, where rate_cats is the number of different rate categories. The array of probability matrices is indexed from 0 to prob_matrices-1. Each matrix entry consists of sufficient space to accommodate rate_cats matrices, which are stored consecutively in memory. Note that libpll will not allocate space for the different substitution matrices specified by rate_matrices. The user must indicate that to libpll by multiplying prob_matrices with the corresponding factor. Finally, scale_buffers sets the number of scaling buffers to be allocated, and attributes states the hardware acceleration options to be used (see Partition Attributes). The function returns a pointer to the allocated pll_partition_t structure. Note that, rate_matrices are used to address heterotachy, i.e. transition probability matrices computed from different rate matrices. For more information, see Updating transition probability matrices.

void pll_partition_destroy(pll_partition_t * partition);

Deallocates all data associated with the partition pointed by partition.

int pll_set_tip_states(pll_partition_t * partition, unsigned int tip_index, const unsigned int * map, const char * sequence);

Set the tip CLV (or tip character array) with index tip_index of instance partition, according to the character sequence sequence and the conversion table map, which translates (or maps) characters to states. For an example see Setting CLV vectors at tips from sequences and maps.

int pll_set_tip_clv(pll_partition_t * partition, unsigned int tip_index, const double * clv);

Set the tip CLV with index tip_index of instance partition, to the contents of the array clv. For an example see Setting CLV vectors manually. Note, this function cannot be used in conjunction with the PLL_ATTRIB_PATTERN_TIP (see Partition Attributes).

void pll_set_subst_params(pll_partition_t * partition, unsigned int params_index, const double * params);

Sets the parameters for substitution model with index params_index, where params_index ranges from 0 to rate_matrices-1, as specified in the pll_partition_create() call. Array params should contain exactly (states*states-states)/2 parameters of type double. These values correspond to the upper triangle elements (above the main diagonal) of the rate matrix.

void pll_set_frequencies(pll_partition_t * partition, unsigned int params_index, const double * frequencies);

Sets the base frequencies for the substitution model with index params_index, where params_index ranges from 0 to rate_matrices-1, as specified in the pll_partition_create() call. The array of base frequencies (frequencies) is copied into the instance. The order of bases in the array depends on the encoding used when converting tip sequences to CLV. For example, if the pll_map_nt map was used with the pll_set_tip_states() function to describe nucleotide data, then the order is A, C, G, T. However, this can be arbitrarily set by adjusting the provided map.

void pll_set_pattern_weights(pll_partition_t * partition, const unsigned int * pattern_weights);

Sets the vector of pattern weights (pattern_weights) for partition. The function reads and copies the first partition->sites elements of pattern_weights into partition->pattern_weights.

void pll_set_category_rates(pll_partition_t * partition, const double * rates);

Sets the rate categories for partition. The function reads and copies the first partition->rate_cats elements of array rates into partition->rates.

int pll_update_invariant_sites(pll_partition_t * partition);

Updates the invariant sites array partition->invariant, according to the sequences in the partition. This function is implicitly called by pll_update_invariant_sites_proportion() when the specified proportion of invariant sites is greater than zero, but it must be explicitly called by the client code if the sequences change.

int pll_update_invariant_sites_proportion(pll_partition_t * partition, unsigned int params_index, double prop_invar);

Updates the proportion of invariant sites for the partition rate matrix with with index params_index. Note that, this call will not implicitly update the transition probability matrices computed from the particular rate matrix, but must be done explicitly for example with a call to pll_update_prob_matrices().

int pll_update_prob_matrices(pll_partition_t * partition, const unsigned int * params_index, const unsigned int * matrix_indices, const double * branch_lengths, unsigned int count);

Computes the transition probability matrices specified by the count indices in matrix_indices, for all rate categories. A matrix with index matrix_indices[i] will be computed using the branch length branch_lengths[i]. To compute the matrix for rate category j, the function uses the rate matrix with index params_indices[j]. Matrices are stored in partition->pmatrix[matrix_indices[i]]. Note that, each such entry holds the matrices for all rate categories, stored consecutively in memory.

int pll_update_eigen(pll_partition_t * partition, unsigned int params_index);

Updates the eigenvectors (partition->eigenvecs[params_index]), inverse eigenvectors (partition->eigenvecs[params_index]), and eigenvalues (partition->eigenvals[params_index]) using the substitution parameters (partition->subst_params[params_index]) and base frequencies (partition->frequencies[params_index]) specified by params_index.

void pll_show_pmatrix(pll_partition_t * partition, unsigned int index, unsigned int float_precision);

Prints the transition probability matrices for each rate category of partition associated with index to standard output. The floating point precision is dictated by float_precision.

unsigned int pll_count_invariant_sites(pll_partition_t * partition, unsigned int * state_inv_count);

Returns the number of invariant sites in the sequence alignment from partition. The array state_inv_count must be of size partition->states and is filled such that entry i contains the count of invariant sites for state i.

int pll_update_invariant_sites(pll_partition_t * partition);

Updates the invariant sites array partition->invariant, according to the sequences in the partition. This function is implicitly called by pll_update_invariant_sites_proportion() when the specified proportion of invariant sites is greater than zero, but it must be explicitly called by the client code if the sequences change.

int pll_update_invariant_sites_proportion(pll_partition_t * partition, unsigned int params_index, double prop_invar);

Updates the proportion of invariant sites for the rate matrix of partition with index params_index. Note that, this call will not implicitly update the transition probability matrices computed from the particular rate matrix, but must be done explicitly for example with a call to pll_update_prob_matrices().

void pll_update_partials(pll_partition_t * partition, const pll_operation_t * operations, unsigned int count);

Updates the count conditional probability vectors (CPV) defined by the entries of operations, in the order they appear in the array. Each operations entry describes one CPV from partition. See also pll_operation_t.

void pll_show_clv(pll_partition_t * partition, unsigned int clv_index, int scaler_index, unsigned int float_precision);

Prints to standard output the conditional probability vector for index clv_index from partition, using the scale buffer with index scaler_index. If no scale buffer was used, then scaler_index must be passed the value PLL_SCALE_BUFFER_NONE. The floating precision (number of digits after decimal point) is dictated by float_precision. The output contains brackets, curly braces and round brackets to separate the values as sites, rate categories and states related, respectively.

double pll_compute_root_loglikelihood(pll_partition_t * partition, unsigned int clv_index, int scaler_index, const unsigned int * freqs_index, double * persite_lnl);

Evaluates the log-likelihood of a rooted tree, for the vector of conditional probabilities (partials) with index clv_index, scale buffer with index scaler_index (or PLL_SCALE_BUFFER_NONE), and base frequencies arrays with indices freqs_index (one per rate category). If persite_lnl is not NULL, then it must be large enough to hold partition->sites double-precision values, and will be filled with the per-site log-likelihoods.

double pll_compute_edge_loglikelihood(pll_partition_t * partition, unsigned int parent_clv_index, int parent_scaler_index, unsigned int child_clv_index, int child_scaler_index, unsigned int matrix_index, const unsigned int * freqs_index, double * persite_lnl);

Evaluates the log-likelihood of an unrooted tree, by providing the conditional probability vectors (partials) for two nodes that share an edge with indices parent_clv_index resp. child_clv_index, scale buffers with indices parent_scaler_index resp. child_clv_index (or PLL_SCALE_BUFFER_NONE), the transition probability matrix with index matrix_index and base frequencies arrays with indices freqs_index (one per rate category). If persite_lnl is not NULL, then it must be large enough to hold partition>sites` double-precision values, and will be filled with the per-site log-likelihoods.

AVAILABILITY¶

Source code and binaries are available at <https://github.com/xflouris/libpll>.

COPYRIGHT¶

Copyright (C) 2015-2017, Tomas Flouri, Diego Darriba

All rights reserved.

Contact: Tomas Flouri <Tomas.Flouri@h-its.org>, Scientific Computing, Heidelberg Insititute for Theoretical Studies, 69118 Heidelberg, Germany

This software is licensed under the terms of the GNU Affero General Public License version 3.

GNU Affero General Public License version 3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

VERSION HISTORY¶

New features and important modifications of libpll (short lived or minor bug releases may not be mentioned):