HAlign-G is a tool written in C++ for aligning multiple gemones. It runs on Linux and Windows.
1.Install WSL for Windows. Instructional video 1 or 2 (Copyright belongs to the original work).
2.Download and install Anaconda. Download Anaconda for different systems here. Instructional video of anaconda installation 1 or 2 (Copyright belongs to the original work).
3.Install HAlign-G.
#1 Create and activate a conda environment for HAlign-G
conda create -n haligng_env
conda activate haligng_env
#2 Add channels to conda
conda config --add channels malab
conda config --add channels conda-forge
#3 Install HAlign-G
conda install -c malab -c conda-forge halign-g
#4 Test HAlign-G
halign-g -hUsage of halign-g2:
halign-g Input_file Output_file [-r/--reference val] [-p/--threads val] [-bwt/--bwt val] [-dc/--divide_conquer val] [-sv/--svLen val] [-h/--help]
Input_file : Input file/folder path[Please use .fasta as the file suffix or a forder]
Output_file : Output file path[Please use .maf or .fasta as the file suffix]
-r/--reference : The reference sequence name [Please delete all whitespace] (defualt value:[Longest])
-p/--threads : The number of threads (defualt value:1)
-bwt/--bwt : The global BWT threshold (defualt value:15)
-dc/--divide_conquer : The divide & conquer Kband threshold (defualt value:10000)
-sv/--svLen : The structure variation length threshold (defualt value:200)
-h/--help : Show this help message (defualt value:false)
HAlign-G1 is designed for multiple sequence alignment (MSA). Among the three versions, it provides the highest alignment quality and supports both FASTA and MAF formats.
Usage of halign-g2:
halign-g2 Input_file Output_file [-r/--reference val] [-p/--threads val] [-dc/--divide_conquer val] [-h/--help]
Input_file : Input file/folder path[Please use .fasta as the file suffix or a forder]
Output_file : Output file path[Please use .maf or .fasta as the file suffix]
-r/--reference : The reference sequence name [Please delete all whitespace] (defualt value:[Longest])
-p/--threads : The number of threads (defualt value:1)
-dc/--divide_conquer : The divide & conquer Kband threshold (defualt value:10000)
-h/--help : Show this help message (defualt value:false)
HAlign-G2 is tailored for multi-genome alignment within the same species. It is optimized to detect a greater number of structural variations, while also supporting both FASTA and MAF formats.
Usage of halign-mum:
halign-mum Input_file Output_file [-r/--reference val] [-t/--threads val] [-l/--load val] [-f/--filter val] [-m/--memory val] [-h/--help]
Input_file : Input folder path
Output_file : Output file path[Please use .maf or .hal as the file suffix]
-r/--reference : The reference file name (defualt value:[Longest])
-t/--threads : The number of threads (defualt value:32)
-l/--load : Whether the second run and the result directory has a postfix structure file (defualt value:0)
-f/--filter : Filter-level: 0-None, 1-General, 2-Strict (defualt value:2)
-m/--memory : Maximum available memory / GB (defualt value:28)
-h/--help : Show this help message (defualt value:false)
HAlign-MUM is part of the HAlign-G2 framework, built on the same algorithmic logic, but extended to support cross-species genome alignment. Unlike HAlign-G1 and G2, it only supports the MAF format.
The software tools are developed and maintained by ZOU's lab.
More tools and infomation can visit our github.