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 and Fudan University, Shanghai.

Main Programs

• cvtree: the main program, it get the phylogenetic tree from the fasta files of genomes.
• g2dv: 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 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.

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