DomRates-Seq

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Modularity is an important keystone in molecular evolution and indispensible for evolutionary innovation. Protein domains as the modules of proteins can be reused in different molecular contexts and therefore rearrangements of domains can create a broad functional diversity with just a few mutational steps. DomRates-Seq infers these rearrangement events of protein domains for a given phylogeny and calculates the rates of the related events.

DomRates-Seq Illustration: (A) shows the Inference of different rearrangement events for an example phylogeny with different insect species via DomRates-Seq. (B) lists all six different single-step events DomRates-Seq takes into account. Those steps can also be combined to form a multi-step event.

DomRates-Seq Illustration: (A) shows the Inference of different rearrangement events for an example phylogeny with different insect species via DomRates-Seq. (B) lists all six different single-step events DomRates-Seq takes into account. Those steps can also be combined to form a multi-step event.

Compared to DomRates, DomRates-Seq is able to solve ambiguous events using sequence information. Also it implements multi-step events.

A UserManual is available here.

Download & Setting up

Requirements

Although we try to keep the dependencies to a minimum some existing libraries are needed.

Optional:

In most Linux distributions (e.g. Ubuntu, Arch Linux) it should be possible to install most of these dependencies using the package manager.

Download

There are two ways to download DomRates-Seq. Either you can download it using git or manually from the website. Both ways are described below.

Tip

If you use git you can easily update to a newer version when available.

Download using git

Use git to clone the repository and download BioSeqDataLibrary as a submodule:

git clone https://zivgitlab.uni-muenster.de/domain-world/domratesseq.git
cd domratesseq

Compilation & Installation

Inside the source folder a build directory is needed in which the code will be compiled. CMake is used to find all the needed requirements of the library.

cmake -S . -B build
cmake --build build

Updating

Sometimes it will be necessary to update DomRates-Seq if it contains some new features or because we unfortunately had a bug somewhere that we have now fixed. If you used git for the original download you can simply use git to update your code. Simply change into the DomRates-Seq directory and type:

git pull
git submodule foreach git pull origin master

You now simply follow again the steps in the Installation section. If you downloaded the code without git you will have to download the latest version and replace the old one with it.

Contact the developer

If you find a problem, have questions or any kind of comment please contact us (domainworld[@]uni-muenster.de).