CyBayes

Features

• Performs MCMC based phylogenetics.
• Can handle multistate characters.
• Can handle polymorphism (or synonymous states of a concept).
• Can handle Jukes-Cantor, Felsenstein-81 models.
• Handles only Rooted trees like in linguistics. So, the trees will have branch lengths and a root.
• Handles trees like Phylo class in ape package of R.

Parameter space moves

• Performs tree moves using external SPR and NNI.
• Branch lengths are sampled according to a exponential distribution.
• Substitution parameters are sampled using Dirichlet and DualSampler move.

Usage

Compile code using python setup.py build_ext --inplace

 usage: mat_mcmc_gamma.py [-h] [-i INPUT_FILE] [-m MODEL] [-n N_GEN] [-t THIN]
                         [-d DATA_TYPE] [-o OUTPUT_FILE]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_FILE, --input_file INPUT_FILE
                        Input a file in Phylip format with taxa and characters
                        separated by a TAB character
  -m MODEL, --model MODEL
                        JC/F81/GTR
  -n N_GEN, --n_gen N_GEN
                        Number of generations
  -t THIN, --thin THIN  Number of generations after to print to file
  -d DATA_TYPE, --data_type DATA_TYPE
                        Type of data if it is binary/multistate. Multistate
                        characters should be separated by a space whereas
                        binary need not be. Specify bin for binary and multi
                        for multistate characters or phonetic alignments
  -o OUTPUT_FILE, --output_file OUTPUT_FILE
                        Name of the out file prefix

  

Linguistic datasets are quite different from biological morphological datasets. A Jukes-Cantor model where all the transition rates are the same is useful for estimating trees with branch lengths.

Example Usage:

python3 mat_mcmc_gamma.py -i data/narrow.phy -m F81 -n 100000 -t 1000 -d bin -o narrow

Output

• Returns a .params file that can be viewed in [Tracer] (http://tree.bio.ed.ac.uk/software/tracer/). The .params file consists of the likelihood and the tree length for each state.
• Returns a .trees file that can be viewed in [FigTree] (http://tree.bio.ed.ac.uk/software/figtree/).

Tested with

• Python3
• Scipy (0.18.1)
• Numpy (1.12.0)