abpoa

abPOA: adaptive banded Partial Order Alignment

Updates (v1.5.6)

• Allow easy incremental MSA
• Add pyproject.toml for pyabpoa

Getting started

Download the latest release:

wget https://github.com/yangao07/abPOA/releases/download/v1.5.6/abPOA-v1.5.6.tar.gz
tar -zxvf abPOA-v1.5.6.tar.gz && cd abPOA-v1.5.6

Make from source and run with test data:

# Linux or MacOS with armv8
make; ./bin/abpoa ./test_data/seq.fa > cons.fa

# MacOS with armv7
make armv7=1; ./bin/abpoa ./test_data/seq.fa > cons.fa

Or, install via conda and run with test data:

conda install -c bioconda abpoa
abpoa ./test_data/seq.fa > cons.fa

Table of Contents

• abPOA: adaptive banded Partial Order Alignment
• Updates (v1.5.6)
• Getting started
• Table of Contents
• Introduction
• Installation

• Installing abPOA via conda/brew
• Building abPOA from source files
• Pre-built binary executable file for Linux/Unix or MacOS
• General usage
• Generate a consensus sequence
• Generate multiple consensus sequences

• Generate row-column multiple sequence alignment in FASTA format
• Generate graph information in GFA format
• Align sequence to an existing graph in GFA/MSA format
• Generate a consensus sequence for amino acid sequences
• Generate a plot of the alignment graph
• Input

• Output
• Consensus sequence
• Row-column multiple sequence alignment
• Full graph information
• Plot of alignment graph
• Algorithm description

• Adaptive banding
• Minimizer-based seeding mode
• Minimizer-based progressive tree
• Multiple consensus sequences
• For development
• Evaluation datasets

• Contact

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