dreamfishes / mcmctree_tree_prep

making input tree for mcmctree

Overview

mcmctree_tree_prep is a tool to prepare input tree files for mcmctree in the PAML package. This program allows to introduce fossil constraints in a command-line interface for the divergence time estimation subsequently done by mcmctree. This script has been tested with PAML 4.9 and supports:

• Lower bound
• Upper bound
• Pair bound
• Point estimate

Parameters such as tail probability can be specified. See PAML MANUAL for details.

Input file

• A rooted tree in the newick format. The input tree can contain support values and branch lengths, which will be removed from the output to be compatible with mcmctree.

Dependency

• python 3.x
• ete3

Usage

See complete options by typing mcmctree_tree_prep.py -h after downloading the script.

Example

You can use pipes to add multiple constraints. --add_header should be specified only in the final step.

python mcmctree_tree_prep.py \
--left_species Populus_trichocarpa \
--right_species Arabidopsis_thaliana \
--lower_bound 100 \
--upper_bound 120 \
--tree input.nwk \
| python mcmctree_tree_prep.py \
--left_species Aquilegia_coerulea \
--right_species Arabidopsis_thaliana \
--lower_bound 130 \
--upper_bound 130 \
--tree - \
--add_header \
> output.nwk

input.nwk

(Aquilegia_coerulea:0.23566,((Arabidopsis_thaliana:0.366634,Populus_trichocarpa:0.167905)100:0.0447481,Vitis_vinifera:0.139353)99:0.0680463)1:0;

output.nwk

4 1
(Aquilegia_coerulea,((Arabidopsis_thaliana,Populus_trichocarpa)'B(100, 120, 0.025, 0.025)',Vitis_vinifera))'@130';

Licensing

This program is BSD-licensed (3 clause). See LICENSE for details.