Collapse Lineage Tree

CLTree is a tool to annotate the phylogenetic tree by lineage and measure their differences in topology by Shannon entropy.

Program and Tasks

All tasks are run by the program cltree with tasks. The available tasks are:

• run: the main program, annotate the tree (newick format) by the lineage of genomes, and statistics. It can be emitted.
• cache: A tool to convert the NCBI taxonomy database dump file (download from:
  NCBI Taxonomy dump to an input lineage string file
• search: Query the lineage of genomes from the NCBI database and Lineage files.
• leaf: Obtain the leaf name list of a phylogenetic tree (in Newick form).

Installation

Compile with CMake

Preparation

• cmake >= 3.0
• compiler supporting C++11 standard
• require library: libz, nlohmann-json

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 Programs in Docker

Docker allows users preforming programs on both Windows and Linux/MacOS. You can download docker free and reference docker document to install it. After installing docker, basic usages for CVTree are:

1. Build/download docker image: docker build -t="cltree-img" . or docker pull ghzuo/cltree. In this step, an image with cltree programs will obtain. Here option "-t" sets the image name. After building the image, you can delete the dangling images for build by docker image prune.
2. Start container from the image in: docker run --rm -it -v $PWD/example:/root/data cltree-img In this step, you will enter the cltree container, and the "example" folder in the host will be mounted on the "data" folder in the container. Change the path to the data folder, and run cltree. You will get the result for genomes in the "list" file. You can change the path "$PWD/example" to your data directory.
3. Exit and stop container: exit in docker terminal.
4. Run cvtree in docker by one command in example folder: docker run --rm -v $PWD:/root/data cltree-img cltree
5. More usage for docker can reference docker document.

Run Programs with Example

If this is the first time you use CLTree package, please go to the "example" folder. Download the taxdump.tar.gz file from NCBI FTP. Run the collapse command to get an annotated phylogenetic tree and monophyly status by:

../build/bin/cltree

More detail of the command usages can be obtained by -h option. To speedup the process, you can get the database image the data by cltree cache command at first, and with option (-I) to output the newick tree and annotate files for handling tree on iTOL.

Reference

• Guanghong Zuo (2022) CLTree: Annotate Phylogenetic Tree by Lineage and Measure their Consistency based on Shannon Entropy. In preparation.
• 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

This software is free for non-commercial use. For commercial use, a software agreement is required.