# CVTree

**Repository Path**: ghzuo/CVTree

## Basic Information

- **Project Name**: CVTree
- **Description**: A whole-genome and alignment-free prokaryotic phylogeny tool
- **Primary Language**: C++
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-01-15
- **Last Updated**: 2025-09-21

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# CVTree

CVTree stands for `Composition Vector Tree` which is the implementation
of an alignment-free algorithm to generate a dissimilarity matrix from
comparatively large collection of DNA or Amino Acid sequences,
preferably whole-genome data, for phylogenetic studies.

Please visit our webserve of CVTree, where you can use the cvtree tools
more convenient. The CVTree3 Web Server have two identical but independent
installations at [Beijing Institute of Genomics, Beijing](http://bigd.big.ac.cn/cvtree)
and  [Fudan University, Shanghai](http://tlife.fudan.edu.cn/cvtree).

## Main Programs

- cvtree: the main program, it get the phylogenetic tree from the fasta files of genomes.
- g2cv: Get the composition vectors based on the fasta files of genomes.
- cv2dm: Get the distance matrix based on the compostion vectors
- dm2tree: Get the phylogenetic tree based the dissimilarity matrix.
- cvdump: Show composition vector
- mconv: convert formats of dissimilarity matrix file
- getdist: Show select dissimilarity from the disimilarity matrix
- diffmtx: compare two dissimilarity matrixes

## Installation

### Compile with CMake

#### Preparation

- cmake >= 3.0
- g++ >= 4.8 or other compiler supporting C++11 standard
- require ligrary: libz
- compiler with support openmp for parallel (_option_)
- Library (_option_): netcdf, netcdf_cpp
- Library (_option_): libhdf5 for c++ (_Please don't use the hdf5 libraries in Anaconda_)

#### Compiling

1. unzip the package file and change into it
2. mkdir build and change into it
3. cmake .. or add some options you wanted
4. make
5. make install (_option_)

### Run Programms in Docker

Docker allows users run programs on both Windows and Linux/MacOS.
You can download docker free and reference [docker document](https://docs.docker.com/install/)
to install it. After install docker, basic usages for CVTree are:

1. Build/download docker image: `docker build -t="cvtree-img" .`
   or `docker pull ghzuo/cvtree`. In this step, a image with cvtree
   programs will obtained. Here option "-t" set the image name. After build
   image, you can delete the dangling images for build by `docker image prune`.
2. Start container from image:
   `docker run --rm -it -v $PWD/example:/root/data cvtree-img`
   In this step, you will enter the cvtree container, and the "example" folder
   of this project will be find in the "data" folder. Change path to the data folder,
   and run `cvtree -G faa`. You will get the result for eight genomes in the "list"
   file. You can change the path "\$PWD/example" to your own data directory.
3. Exit and stop container: `exit` in docker terminal.
4. Run cvtree in docker by one command:
   `docker run --rm -v $PWD:/data -w /data cvtree-img cvtree -G faa`
5. More usage for docker can reference [docker document](https://docs.docker.com/).

### Run Programs in Singularity

1. save the image as tar file: `docker save -o cvtree.tar cvtree-img`
2. write a singularity definition file named `cvtree.def` like this:

```plain
bootstrap: docker-archive
from: cvtree.tar

%runscript
    sh -c "$*"
```

3. convert cvtree.tar to cvtree.sif by:
    `singularity build --fakeroot cvtree.sif cvtree.def`
    and place the `cvtree.sif` in the `$PATH` directory.
4. run cvtree program: `cvtree.sif cvtree -G faa`

## Run Programs with Example

If this is the first time you use CVTree package, please go to the
"example" folder. Edit "list" to include the genome names, and run
the cvtree command to get the phylogeny tree by:

    ../build/cvtree -G faa

More detail of the command usage can be obtaion by `-h` option.

## Reference

- Guanghong Zuo (2021) CVTree: A Parallel Alignment-free Phylogeny
  and Taxonomy Tool based on Composition Vectors of Genomes,
  BioRxiv doi:10.1101/2021.02.04.429726
- Ji Qi, Bin Wang, Bailin Hao (2004) Whole proteome prokaryote phylogeny
  without sequence alignment: a K-string composition approach, J Mol
  Evol, 58: 1–11
- Guanghong Zuo, Bailin Hao (2015) CVTree3 web server for
  whole-genome-based and alignment-free prokaryotic phylogeny and
  taxonomy, Genomics Proteomics & Bioinformatics, 13: 321-331

## License

MIT license