WMSA

A method of Multiple Sequence Alignment, which the writer is Wym6912.

Recommended environment

Liunx-based systems, like Ubuntu, CentOS .

If you are a Windows 10 user, you can use it by WSL (Manually download Windows Subsystem for Linux (WSL) Distros | Microsoft Docs).

How to use this program

Directly clone and complie the project (Recommended for macOS users)

git clone github.com/wym6912/WMSA --recursive 
# add --recursive arugment to get cd-hit and mafft subprograms
make all THREADS=16 # not -j16 because the THREADS=16 can be used by the subprograms
make install # program is installed on /usr/bin by default
wmsa -H # help message on this program

You also can download source code on the release.

If you are an MACOS user, please use the following make command:

make all THREADS=16 NOOPENMP=yes

in order to avoid the bug on openmp library.

Download from conda (Recommended for Linux users)

We recommended use conda to configuration for Linux users. See Install Miniconda if not installed conda or miniconda before. The command of configuration like this:

conda create -n wmsa # make an new environment for running wmsa
conda activate wmsa
conda install wmsa -c wym6912
wmsa -H

How to run the method on a test set

The test data is published here.

You can clone and use the following project by using this command:

git clone https://github.com/malabz/WMSA-dataset
# test mt1x dataset on WMSA
cd WMSA-dataset/mt/
unzip mt1x.zip
/usr/bin/wmsa -i mt1x.fasta -o mt1x.wmsa.fasta -T 16 -c 0.9

The arugments in last line means the input file ( -i ) is mt1x.fasta, the output file ( -o ) is mt1x.wmsa.fasta, use 16 threads ( -T ) and the similarity of cd-hit ( -c ) in wmsa is 0.9.

For dataset from www.drive5.com/bench, see here for testing in wmsa .

How to interpret the results

For mt and SARS-COV-2 test case, we use SP Score to measure the result. The SP Score script can be found here.

Use the script test the result by changing the arguments with modifing the match ( --match ) score equals to 1 and all mismatch conditions (like mismatch --mismatch , gap with character --gap1 and gap with gap --gap2 ) score equals to 0:

wget https://github.com/malabz/MSATOOLS/raw/main/SPscore/SPscore.py
python3 SPscore.py --input mt1x.wmsa.fasta --match 1 --mismatch 0 --gap1 0 --gap2 0

How to upgrade this program

git pull
git submodule foreach 'git pull'

...or you can download source code on the release.

How to remove this program

make uninstall