Detecting trait-dependent evolutionary rate shifts in sequence sites Prof. Itay Mayrose Lab - Plant Evolution, bioinformatics, & comparative genomics
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Overview

• A rooted ultrametric phylogentic tree with branch lengths (Newick)
• A multiple sequence alignment (MSA) of the sequence data of the extant species (Fasta)
• The character states of the extant species coded as either '0' or '1' (Fasta)

1. Downloading and compiling the program
2. Usage
   

1. Download the TraitRateProp source code or a pre-compiled version for UNIX

If you choose to use the pre-compiled file you might need to set execution permissions for it (chmod +x PRE-COMPILED)

If you choose to compile yourself, follow these steps:


2. In order to unzip and untar the files, type:
tar -xzf TraitRateProp_source_20161221.tar.gz

This will create the directory TraitRateProp_source_20161221


3. Compile the software by typing (we used the gcc620 compiler, you'll need at least gcc480):
cd TraitRateProp_source_20161221/libs/phylogeny
make doubleRep
cd ../../programs/TraitRateProp/
make doubleRep

(Running 'make' takes a while, warnings issued can be ignored)

Small run example

1. Create a directory for the example (mkdir EXAMPLE_DIRECTORY)
2. Download the example input MSA file to EXAMPLE_DIRECTORY
3. Download the example input trait states file to EXAMPLE_DIRECTORY
4. Download the example input tree file to EXAMPLE_DIRECTORY
5. Download the example input TraitRateProp configuration file to EXAMPLE_DIRECTORY
6. Edit the example TraitRateProp configuration file by replacing "FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY" with the full path to the example directory you created
   This edit will require 5 changes in the example TraitRateProp configuration file
7. Run TraitRateProp with the edited configuration file:
   TraitRateProp_source_20161221/programs/TraitRateProp/traitRate.doubleRep EXAMPLE_DIRECTORY/example_TRP_configuration_file.txt

TraitRateProp's output files

TraitRateProp produces three output files of interest:

1. The alternative results file (set in _outFile ) – contains information about the parameter estimations under the alternative model (TR or TRP) and the log-likelihood scores of the null model (model 0) and the alternative model. These scores can be used for the chi-sq LRT.
2. The null results file (set in _outFileNullParams) – contains the null model parameter estimations.
3. The position likelihoods file (set in _LLPerPositionFile) – in the TRP alternative model, the likelihood of each position is computed once with no association between the rate and the phenotypic trait and once with such an association. This file contains these computations for each position and the ratio between them (= the Bayes factor).

Summarizing the results of the first two output files in a friendly format is possible with this Perl script.
Running this script will produce an output in this format.

Summarizing the per-position predictions based on the second two output files is possible with this Perl script.
Running this script will produce an output in this format.

Running TraitRateProp on your own input

We refer you to the TraitRateProp manual where you can find a full description of the program's input configuration.
We also provide a set of template configuration files. The details concerning these also appear in the manual.