bs_inBV

A tool with which the branch lengths, gradient, and Hessian used by MCMCtree to approximate the likelihood calculation are estimated with complex amino acid substitution models. Particularly, bs_inBV will return the in.BV file with the inferred branch lengths, gradient, and Hessian; the latter is approximated using a bootstrap approach.

Idea

People have increasingly acknowledged the importance of using more complex amino acid substitution models in modeling sequence evolution, particularly when analysing deep phylogenies. MCMCtree supports various amino acid substitution models, being LG+F the most complex one. Nevertheless, more complex models are available in other phylogenetic software such as IQ-TREE and PhyML among others.

When enabling the approximate likelihood calculation with MCMCtree (i.e., usedata = 2 followed by usedata = 3; please consult the PAML documentation for details), CODEML (BASEML if nucleotide data) will be first "called" by MCMCtree when using usedata = 2 to estimate the branch lengths, the gradient, and the Hessian under a maximum-likelihood approach; vectors and matrix that will be output in the so-called in.BV file. Subsequently, MCMCtree will use the branch lengths, gradient, and Hessian in this in.BV file to approximate the likelihood calculation during the MCMC when enabling usedata = 3 in the control file. Particularly, bs_inBV has been written to use complex amino acid substitution models available in IQ-TREE to estimate the branch lengths and approximate the Hessian matrix by calculating the negative inverse of the bootstrap covariance matrix of branch length estimates. In addition, bs_inBV will then set all the elements of the gradient vector to zero.

Installation

Ruby gems

First and foremost, please make sure that Ruby is installed. Second, it is recommended to have Ruby v3.x installed but earlier version should also work if the following gems are installed.

In addition, you will need to install the following gems before running bs_inBV using the command gem install <gem_name>. The gems to be installed are the following:

• parallel
• colorize
• find
• getoptlong
• time
• fileutils
• tmpdir
• bio
• bio-nwk

Third-party tools

In order to run bs_inBV, you will need to install the following programs:

• PAML. Please refer to the PAML Wiki for more details regarding the installation procedure.
• IQ-TREE. Please refer to the IQ-TREE website for more details regarding the installation procedure.
• newick-utils. If you had any issues when installing newick-utils from the source code, please download the pre-compiled binaries of Newick Utilities v1.6. These binaries are available on this website.
• R. Please make sure that you follow the installation instructions on the main website. WSL users will need to install R via the terminal too. In addition, please make sure that the MASS R package is installed as it is used by script reorder_node.rb.

Changes to ruby scripts prior to running bs_inBV

At the time of writing, bs_inBV has pre-defined some paths an aliases to execute third-party tools in some of its ruby scripts. If you are to use this tool under a different environment, please make sure you change the following lines to match your PC settings:

• Users will need to update the path to PAML programs in line 40 in script do_mcmctree.rb. If users have an alias to execute MCMCtree, they may also have to change line 43 accordingly.
• If users have not exported IQ-TREE to their PATH or have an alias different from the one specified in line 26 in script create_hessian_by_bootstrapping.rb, they will need to change that too. The same applies to lines 27-28 for newick-utils programs and line 29 for MCMCtree in that same script.

Usage

• If you have already run MCMCtree and have the in.BV file, please run the following command to obtain a "reference" tree that will be subsequently used by bs_inBV:

  sed '4!d' in.BV > ref.tre

• If you do not have an in.BV file, then you can run a quick dummy analysis with MCMCtree to obtain one. Note that the main reason for running this program now is just to make sure that the order of the tips that will be output in the in.BV is the same as that of the input tree file specified by the user. To save time, you can ask MCMCtree to sample from the prior (i.e., no data will be used, set usedata = 0 in the control file) and specify few iterations (e.g., set burnin = 1, sampfreq = 1, nsample = 1 in the control file). If you are using the control file given in the example directory, please also make sure that you set usedata = 2. If you have your own control file, please make the changes accordingly. Once you have a "dummy" in.BV file, you can extract the "reference" tree:

  sed '4!d' in.BV > ref.tre

• Now, you are ready to run bs_inBV! Please execute this tool by running the following command (make sure that the paths to the third-party tools have been modified to match your settings as aforementioned):

  # Run from the same directory where you have this script
  # You can use relative/absolute paths to your input files
  ruby create_hessian_by_bootstrapping.rb --ali <path_to_alignment_file> --calibrated_tree <path_to_calibrated_tree_file> --outdir <path_to_output_directory> --ref <path_to_reference_tree>/ref.tre --force -b 1000 --cpu <number_CPUs_for_IQTREE_to_use> -m LG+G+C20 --mcmctree_ctl <path_to_MCMCtree_control_file>/mcmctree.ctl --run_mcmctree --pmsf

  Options:

  • --ali: path to alignment file.
  • --calibrated_tree: path to input calibrated tree file that will be used by MCMCtree.
  • --outdir: path to the output directory.
  • --force: tells the program to overwrite the output files, if any.
  • -b: number of bootstraps that IQ-TREE will run. Please note that only traditional bootstrapping is allowed as the UFB approach implemented in IQ-TREE cannot be used when using a fixed tree topology (which is required by MCMCtree).
  • --cpu: number of cores that will be used by IQ-TREE.
  • -m: amino acid substitution model that IQ-TREE will use for branch lengths inference.
  • --mcmctree_ctl: path to the control file that will execute MCMCtree. Please make sure that this control file has usedata = 2 in.BV if you want to run MCMCtree after bs_inBV outputs the in.BV file (enable this feature by adding option --run_mcmctree).
  • --pmsf: use the PMSF approximation

Example

There is a dataset that you can use in the example directory to test the usage of bs_inBV. First, please clone this repository and follow all the steps detailed above with regards to gems, third-party tools, and code changes during the installation procedure. Once everything is ready, then go to directory example and execute the following command:

# Run this command from directory `example`
ruby ../create_hessian_by_bootstrapping.rb --ali combined.phy --calibrated_tree species.trees --outdir C20 --ref ref.tre --force -b 100 --cpu 8 -m LG+G+C20 --mcmctree_ctl mcmctree.ctl --run_mcmctree --pmsf

Once the command above finishes, you will see the following output files:

• C20/split: this directory will contain all the output files generated by IQ-TREE. The name you choose for option --outdir will be given to the first directory (e.g., C20 in this example).
• C20/mcmctree: if option --run_mcmctree is not enabled, this directory will contain your input files and the in.BV file. If you decide to run MCMCtree by enabling option --run_mcmctree, then you will also find the output files generated by MCMCtree in this directory. Please note that the in.BV file will contain the vector of branch length estimated using the amino acid substitution model defined by the user (e.g.,-m LG+G+C20 in this example), the gradient vector, and the Hessian matrix approximated using a bootstrap approach.

NOTE 1: Please check above to learn how to generate file ref.tre. For more details about how to configure the control file for MCMCtree, please check the PAML documentation.

NOTE 2: The example data were simulated under model LG+C20+G and a root age of 4.0 Ga. For more details about the simulation, please read this blog post.

Notes

1. When using --run_mcmctree, MCMCtree will be execute right after generating the in.BV file. If you only want to obtain the in.BV file based on your specified amino model (e.g., LG+G+C60), please do not use --run_mcmctree.
2. Without --pmsf, IQ-TREE is much slower because the traditional Cxx model is used by IQ-TREE.
3. In case you experience any issues related to inverting the variance-covariance matrix of the branch lengths, please try to (i) increase the number of bootstrap or (ii) avoid including too closely-related species in your phylogeny. However, in the current version (actually since v1.0) the issue of singular covariance matrix is solved by creating a new matrix by adding a small number of diagonal term to the original covariance matrix, so probably no need to worry about it.
4. The tool should in theory work for any substitution models but would be in practice most useful for complex models as these are not included in MCMCtree. It also works for nucleotides in which case however you may need to specify seqtype=1 in the file mcmctree.ctl.
5. For more details, please see Note S4 and Figs. S9-S10 in the original reference (see below).

Acknowledgement

I am particularly grateful for Sandra Álvarez-Carretero and Edmund Moody from University of Bristol for their help in testing the scripts and providing feedback and suggestions. Particularly, Sandra has contributed to some coding and editing Readme.md to make the tool much more user-friendly (see their work for more details).

How to cite

Dating the bacterial tree of life based on ancient symbiosis Sishuo Wang, Haiwei Luo bioRxiv 2023.06.18.545440; doi: https://doi.org/10.1101/2023.06.18.545440.

You may also need to cite corresponding papers for the use of PAML, IQ-TREE, Newick Utilities, and BioRuby.