A tool for phylogenomic tree building. The program estimates species tree, gene trees, gene concordance factor, site concordance factor, and organize resulting files using a single command:
{Bash}
myte auto -d [gene-alignment-folder]
myte is a single executable command line app. The executable file will be available in the release link. Copy it to the folder that is registered in your PATH variable.
OS support:
Dependencies:
You can also compile from source. See segul readme for details instruction on how to install a command line application written in Rust.
Download the rust compiler here and follow the installation instruction.
{Bash}
git clone https://github.com/hhandika/myte
```{Bash} cd myte
cargo build --release ```
Your executable will be available at /target/release/myte. Copy it to the folder that is registered in your PATH variable.
Notes: The program may failed to run in outdated HPC OS due to GLIBC errors. The solution is to compile it to fully static binary using musl compiler. See instruction here. Then, to build the binary cargo build --release --target x86_64-unknown-linux-musl
```{Bash} myte 0.3.2 Heru Handika A tool for phylogenomic tree building
USAGE:
myte
FLAGS: -h, --help Prints help information -V, --version Prints version information
SUBCOMMANDS: auto Auto estimate species tree, gene trees, and gene and site concordance factor check Check dependencies gene Batch gene tree estimation using IQ-Tree help Prints this message or the help of the given subcommand(s) ```
The code is still at infancy. Working features:
{Bash}
myte auto -d [alignment-folder]
The program will create multiple instances of IQ-TREE to run gene tree estimation in parallel. The program assess available cpu resources in your system and does it sensibly. In a simple word, it won't slow down your computer despite using all your cpu cores. Hence, it can be used on a personal computer without interferring your other work.
To generate gene trees:
{Bash}
myte gene -d [alignment-folder]