phylogenetics 0.1.0

Libraries

This package provides the following libraries (via dune):

phylogenetics

Documentation:

• Phylogenetics.Alignment A representation for sequence alignments
• Phylogenetics.Alphabet
• Phylogenetics.Amino_acid
• Phylogenetics.Birth_death
• Phylogenetics.Bppsuite
• Phylogenetics.Codon
• Phylogenetics.Discrete_pd
• Phylogenetics.Dna
• Phylogenetics.Felsenstein Functions that implement Felsenstein's "pruning" algorithm to compute likelihood of phylogenetic trees with known sequences at leaves.
• Phylogenetics.Fitch
• Phylogenetics.ID_monad A state monad to generate integer identifiers
• Phylogenetics.Iupac_nucleotide Nucleotide IUPAC symbol
• Phylogenetics.Linear_algebra This modules wraps linear algebra functions
• Phylogenetics.Linear_algebra_tools This modules wraps linear algebra functions (from Lacaml) and provide a few completely new functions (such as exponentiation)
• Phylogenetics.List1
• Phylogenetics.MCMC
• Phylogenetics.Mutsel https://www.biorxiv.org/content/biorxiv/early/2016/04/30/037689.full.pdf https://academic.oup.com/mbe/article/34/1/204/2656188
• Phylogenetics.Nelder_mead An implementation of Nelder-Mead algorithm for function optimization
• Phylogenetics.Newick
• Phylogenetics.Newick_ast
• Phylogenetics.Newick_lexer
• Phylogenetics.Newick_parser
• Phylogenetics.Newick_parser_errors
• Phylogenetics.Nucleotide A single DNA base
• Phylogenetics.Nucleotide_process A representation of classical parametric processes on nucleotides
• Phylogenetics.Phylip The original format is described there. This implementation also allows a somewhat more relaxed syntax:
• Phylogenetics.Phylo_ctmc
• Phylogenetics.Phylogenetic_tree Module for phylogenetic trees.
• Phylogenetics.Rate_matrix Continuous Time Markov Chain rate matrix
• Phylogenetics.Rejection_sampling
• Phylogenetics.Seq Module for sequences of bases. Provides a functor to build the module for any base module with the BASE signature.
• Phylogenetics.Sequence_generation
• Phylogenetics.Sequence_simulator
• Phylogenetics.Sigs Compilation of module signatures used elsewhere.
• Phylogenetics.Simulator
• Phylogenetics.Site_evolution_model Compilation of modules implementing evolution models and providing relevant mathematical procedure (eg, exponential of transition matrix); also includes functors to build models from transition matrices.
• Phylogenetics.Stat_tools Probability and statistics tools (eg, samplers and distribution handling).
• Phylogenetics.TKF91
• Phylogenetics.Tree
• Phylogenetics.Utils
• Phylogenetics.Wag WAG matrix parser
• Phylogenetics.Zipper Zipper type for fast operations on large phylogenetic trees.

Dependencies: angstrom.unix, biocaml.ez, core_kernel, gsl, lacaml, menhirLib, printbox, ppx_sexp_conv.runtime-lib, ppx_compare.runtime-lib, ppx_enumerate.runtime-lib, ppx_hash.runtime-lib, ppx_here.runtime-lib, ppx_assert.runtime-lib, ppx_bench.runtime-lib, bin_prot, fieldslib, ppx_inline_test.runtime-lib, ppx_module_timer.runtime, typerep, variantslib, ppx_expect.collector, ppx_expect.config, base, base_quickcheck, ppx_deriving.runtime