abPOA

https://github.com/yangao07/abpoa
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abPOA is an adaptive banded Partial Order Alignment tool that performs multiple sequence alignment...
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License:MIT
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### Install pyabpoa from source

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Install pyabpoa from its source code. This method requires git and make, and cython must be installed.

```bash
git clone --recursive https://github.com/yangao07/abPOA.git
cd abPOA
make install_py
```

--------------------------------

### Install abPOA via Homebrew

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Installs abPOA on macOS using Homebrew. Ensure Homebrew is installed and up to date.

```bash
brew install abpoa
```

--------------------------------

### Install pyabpoa with pip

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Install the pyabpoa library using pip. This is the recommended method for most users.

```bash
pip install pyabpoa
```

--------------------------------

### Run example script

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Execute the example script provided within the pyabpoa source code. This script likely demonstrates various functionalities of the library.

```bash
python ./python/example.py
```

--------------------------------

### MSA Input Example for Alignment

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Demonstrates generating an MSA file for a single sequence, which can then be used as input for aligning another sequence.

```bash
abpoa seq1.fa -r1 > seq1.msa
abpoa -i seq1.msa seq2.fa > cons.fa
```

--------------------------------

### Install abPOA via Conda

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Installs abPOA using the bioconda channel. Ensure conda is configured with bioconda.

```bash
conda install -c bioconda abpoa
```

--------------------------------

### Install and Run abPOA via Conda

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Install abPOA using the bioconda channel and then run it with a FASTA file to generate a consensus sequence.

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

--------------------------------

### Install Graphviz for Plotting

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Installs the graphviz package required for generating plots of the alignment graph. This command is for Debian/Ubuntu-based systems.

```bash
sudo apt-get install graphviz
```

--------------------------------

### Download and Extract abPOA Release

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Download the latest release of abPOA and extract the archive. Navigate into the extracted directory to proceed with building or installation.

```bash
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
```

--------------------------------

### Initialize and Configure C API

Source: https://context7.com/yangao07/abpoa/llms.txt

Sets up alignment parameters and context structures. Requires manual memory management using free functions.

```c
#include <stdio.h>
#include <stdlib.h>
#include "abpoa.h"

int main() {
    // Initialize abPOA alignment structure
    abpoa_t *ab = abpoa_init();

    // Initialize parameters with defaults
    abpoa_para_t *abpt = abpoa_init_para();

    // Configure alignment mode
    abpt->align_mode = ABPOA_GLOBAL_MODE;  // 0:global, 1:local, 2:extension

    // Configure scoring parameters
    abpt->match = 2;
    abpt->mismatch = 4;
    abpt->gap_mode = ABPOA_CONVEX_GAP;  // ABPOA_LINEAR_GAP, ABPOA_AFFINE_GAP
    abpt->gap_open1 = 4;
    abpt->gap_ext1 = 2;
    abpt->gap_open2 = 24;
    abpt->gap_ext2 = 1;

    // Configure adaptive banding
    abpt->wb = 10;    // extra_b
    abpt->wf = 0.01;  // extra_f, band width = wb + wf * seq_len

    // Configure output options
    abpt->out_msa = 1;   // Generate row-column MSA
    abpt->out_cons = 1;  // Generate consensus
    abpt->max_n_cons = 1;

    // Apply parameter settings (must call after configuration)
    abpoa_post_set_para(abpt);

    // ... perform alignment ...

    // Cleanup
    abpoa_free(ab);
    abpoa_free_para(abpt);

    return 0;
}
```

--------------------------------

### Download Pre-built Binary for Linux

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Downloads and extracts a pre-compiled abPOA binary for 64-bit Linux systems. Useful if compilation fails.

```bash
wget https://github.com/yangao07/abPOA/releases/download/v1.5.6/abPOA-v1.5.6_x64-linux.tar.gz
tar -zxvf abPOA-v1.5.6_x64-linux.tar.gz
```

--------------------------------

### Download Pre-built Binary for macOS

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Downloads and extracts a pre-compiled abPOA binary for ARM64 macOS systems. Useful if compilation fails.

```bash
wget https://github.com/yangao07/abPOA/releases/download/v1.5.6/abPOA-v1.5.6_arm64-macos.tar.gz
tar -zxvf abPOA-v1.5.6_arm64-macos.tar.gz
```

--------------------------------

### Build abPOA from Source (Release Tarball)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Downloads, extracts, and compiles abPOA from a release tarball. Requires gcc and zlib. Recommended for stable releases.

```bash
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
```

--------------------------------

### Build abPOA from Source (Git Clone)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Clones the abPOA repository and compiles it. Use this for the latest development version. Requires recursive clone.

```bash
git clone --recursive https://github.com/yangao07/abPOA.git
cd abPOA; make
```

--------------------------------

### Compile and Link abPOA C Library

Source: https://context7.com/yangao07/abpoa/llms.txt

Provides bash commands for compiling a C program that uses the abPOA library, linking against the static library, and building abPOA from source. Ensure correct include and library paths are specified.

```bash
# Compile with static library
gcc -g myprogram.c -I./include -L./lib -labpoa -lz -lm -lpthread -o myprogram
```

```bash
# Or link directly with the archive
gcc -g myprogram.c -I./include ./lib/libabpoa.a -lz -lm -lpthread -o myprogram
```

```bash
# Build abPOA from source
git clone --recursive https://github.com/yangao07/abPOA.git
cd abPOA && make
```

```bash
# Install Python bindings
pip install pyabpoa
```

```bash
# Or build from source with cython
cd abPOA && make install_py
```

--------------------------------

### Build abPOA from Source (MacOS ARMv7)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Compile abPOA from source code on MacOS systems with ARMv7 architecture. Use the 'armv7=1' flag during the make process.

```bash
make armv7=1; ./bin/abpoa ./test_data/seq.fa > cons.fa
```

--------------------------------

### Output Alignment Graph and Sequences using C API

Source: https://context7.com/yangao07/abpoa/llms.txt

Demonstrates how to configure and use abPOA C API functions to output alignment graphs in GFA format, consensus sequences, and MSAs to files. Requires initialization of abpoa_t and abpoa_para_t structures.

```c
#include <stdio.h>
#include <stdlib.h>
#include "abpoa.h"

int main() {
    abpoa_t *ab = abpoa_init();
    abpoa_para_t *abpt = abpoa_init_para();

    // Configure for GFA output
    abpt->out_gfa = 1;
    abpt->out_cons = 1;
    abpt->out_msa = 1;
    abpoa_post_set_para(abpt);

    // ... perform MSA ...

    // Output GFA to file
    FILE *gfa_fp = fopen("output.gfa", "w");
    abpoa_generate_gfa(ab, abpt, gfa_fp);
    fclose(gfa_fp);

    // Output consensus sequence
    FILE *cons_fp = fopen("consensus.fa", "w");
    abpoa_output_fx_consensus(ab, abpt, cons_fp);
    fclose(cons_fp);

    // Output row-column MSA
    FILE *msa_fp = fopen("alignment.msa", "w");
    abpoa_output_rc_msa(ab, abpt, msa_fp);
    fclose(msa_fp);

    // Generate alignment graph visualization
    abpt->out_pog = strdup("graph.png");  // or "graph.pdf"
    abpoa_dump_pog(ab, abpt);  // Requires graphviz 'dot' command

    // Combined output (respects out_cons, out_msa, out_gfa flags)
    abpoa_output(ab, abpt, stdout);

    abpoa_free(ab);
    abpoa_free_para(abpt);

    return 0;
}
```

--------------------------------

### Perform initial alignment for incremental updates

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Initializes an alignment process that can be followed by incremental additions. Use `msa_align` to set up the initial alignment before adding more sequences.

```python
pyabpoa.msa_aligner.msa_align(seqs, out_cons, out_msa, max_n_cons=1, min_freq=0.25, incr_fn=b'')
```

--------------------------------

### Perform Incremental MSA in C

Source: https://context7.com/yangao07/abpoa/llms.txt

Demonstrates initializing the abpoa structure, aligning sequences in multiple batches, and cleaning up memory between steps. Ensure abpoa_clean_msa_cons() is called after each batch to avoid memory leaks.

```c
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "abpoa.h"

extern unsigned char nt4_table[256];

int main() {
    int i, j;
    int n_seqs = 10, first_batch = 5, second_batch = 3, third_batch = 2;

    char *seqs[] = {
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT",
        "CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT"
    };

    // Initialize
    abpoa_t *ab = abpoa_init();
    abpoa_para_t *abpt = abpoa_init_para();
    abpt->out_msa = 1;
    abpt->out_cons = 1;
    abpt->max_n_cons = 2;
    abpoa_post_set_para(abpt);

    // Prepare all sequences
    int *seq_lens = malloc(sizeof(int) * n_seqs);
    uint8_t **bseqs = malloc(sizeof(uint8_t*) * n_seqs);
    for (i = 0; i < n_seqs; i++) {
        seq_lens[i] = strlen(seqs[i]);
        bseqs[i] = malloc(sizeof(uint8_t) * seq_lens[i]);
        for (j = 0; j < seq_lens[i]; j++)
            bseqs[i][j] = nt4_table[(int)seqs[i][j]];
    }

    // Step 1: Align first batch
    printf("=== First batch: %d sequences ===\n", first_batch);
    abpoa_msa(ab, abpt, first_batch, NULL, seq_lens, bseqs, NULL, stdout);

    // IMPORTANT: Clean MSA/consensus memory before incremental add
    abpoa_clean_msa_cons(ab);

    // Step 2: Add sequences one by one (disable output for intermediate steps)
    printf("\nGraph has %d sequences, %d nodes\n", ab->abs->n_seq, ab->abg->node_n);
    abpt->out_msa = 0;
    abpt->out_cons = 0;

    for (i = 0; i < second_batch; i++) {
        abpoa_msa(ab, abpt, 1, NULL,
                  seq_lens + first_batch + i,
                  bseqs + first_batch + i,
                  NULL, stdout);
    }

    // Step 3: Add final batch and output results
    printf("\n=== Final batch: %d sequences ===\n", third_batch);
    abpt->out_msa = 1;
    abpt->out_cons = 1;
    abpoa_msa(ab, abpt, third_batch, NULL,
              seq_lens + first_batch + second_batch,
              bseqs + first_batch + second_batch,
              NULL, stdout);

    printf("\nFinal graph: %d sequences, %d nodes\n",
           ab->abs->n_seq, ab->abg->node_n);

    // Cleanup
    for (i = 0; i < n_seqs; i++) free(bseqs[i]);
    free(bseqs);
    free(seq_lens);
    abpoa_free(ab);
    abpoa_free_para(abpt);

    return 0;
}
```

--------------------------------

### Build abPOA from Source (Linux/MacOS ARMv8)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Compile abPOA from source code on Linux or MacOS systems with ARMv8 architecture. After successful compilation, you can run the executable.

```bash
make; ./bin/abpoa ./test_data/seq.fa > cons.fa
```

--------------------------------

### Configure Score Matrix and Parameters

Source: https://context7.com/yangao07/abpoa/llms.txt

Use abpoa_set_mat_from_file to load external scoring matrices and configure gap penalties or adaptive banding for alignment.

```c
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "abpoa.h"

int main() {
    // Initialize
    abpoa_t *ab = abpoa_init();
    abpoa_para_t *abpt = abpoa_init_para();

    // Method 1: Use built-in match/mismatch scores
    abpt->match = 2;
    abpt->mismatch = 4;

    // Method 2: Load score matrix from file
    abpt->mat_fn = strdup("BLOSUM62.mtx");
    abpt->use_score_matrix = 1;
    abpoa_set_mat_from_file(abpt, abpt->mat_fn);

    // Configure gap penalties (convex gap model)
    abpt->gap_mode = ABPOA_CONVEX_GAP;
    abpt->gap_open1 = 4;
    abpt->gap_ext1 = 2;
    abpt->gap_open2 = 24;
    abpt->gap_ext2 = 1;
    // Effective penalty: min(gap_open1 + len*gap_ext1, gap_open2 + len*gap_ext2)

    // Configure adaptive banding
    abpt->wb = 10;     // Base extra band width
    abpt->wf = 0.01;   // Proportional factor
    // Actual band: wb + wf * sequence_length

    // Output settings
    abpt->out_msa = 1;
    abpt->out_cons = 1;

    // Finalize parameters
    abpoa_post_set_para(abpt);

    // ... perform alignment with amino acid sequences ...

    abpoa_free(ab);
    abpoa_free_para(abpt);

    return 0;
}
```

--------------------------------

### Run abPOA via Command Line

Source: https://context7.com/yangao07/abpoa/llms.txt

Perform multiple sequence alignment and consensus calling using the abpoa command-line interface.

```bash
# Basic consensus sequence generation
abpoa seq.fa > cons.fa

# Generate multiple consensus sequences for diploid data
abpoa heter.fa -d2 > 2cons.fa

# Generate row-column multiple sequence alignment in FASTA format
abpoa seq.fa -r1 > out.msa

# Generate MSA with consensus sequence included
abpoa seq.fa -r2 > out_cons.msa

# Generate graph information in GFA format
abpoa seq.fa -r3 > out.gfa

# Generate GFA with consensus path
abpoa seq.fa -r4 > out.gfa

# Use most frequent bases method for consensus
abpoa seq.fa -a1 > cons.fa

# Align sequences to an existing graph
abpoa -i existing.gfa seq.fa -r3 > out.gfa
abpoa -i existing.msa seq.fa -r1 > out.msa

# Generate alignment graph plot (requires graphviz)
abpoa seq.fa -g poa.png > cons.fa

# Process amino acid sequences with scoring matrix
abpoa -c -t BLOSUM62.mtx input_aa.fa > output_aa_cons.fa

# Batch processing with file list
abpoa -l file_list.txt > all_cons.fa
```

--------------------------------

### Perform MSA and print results

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Demonstrates how to perform a multiple sequence alignment using pyabpoa, generate consensus sequences, and print the alignment. Requires importing the pyabpoa library.

```python
import pyabpoa as pa
a = pa.msa_aligner()
seqs=[
'CCGAAGA',
'CCGAACTCGA',
'CCCGGAAGA',
'CCGAAGA'
]
a_res=a.msa(seqs, out_cons=True, out_msa=True) # perform multiple sequence alignment 

for seq in a_res.cons_seq:
    print(seq)  # print consensus sequence

a_res.print_msa() # print row-column multiple sequence alignment in PIR format
```

--------------------------------

### Generate Consensus Sequence (FASTA)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Outputs the consensus sequence in FASTA format. The name field is set to 'Consensus_sequence'.

```text
>Consensus_sequence
ACGTGTACACGTTGAC
```

--------------------------------

### Generate Consensus Sequences with Python

Source: https://context7.com/yangao07/abpoa/llms.txt

Configures consensus generation parameters such as maximum count and frequency thresholds.

```python
result = aligner.msa(
    seqs,
    out_cons=True,
    out_msa=True,
    max_n_cons=2,      # Maximum number of consensus sequences
    min_freq=0.25      # Minimum frequency threshold for each consensus
)

print(f"Generated {result.n_cons} consensus sequences")
for i in range(result.n_cons):
    print(f">Consensus_sequence_{i+1}")
    print(result.cons_seq[i])
    print(f"Length: {result.cons_len[i]}")
```

--------------------------------

### Perform Multiple Sequence Alignment with abpoa_msa

Source: https://context7.com/yangao07/abpoa/llms.txt

This C code demonstrates how to use the abpoa_msa function for multiple sequence alignment. It includes sequence encoding, parameter initialization, execution, and programmatic access to the alignment results. Ensure necessary headers are included and memory is managed properly.

```c
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "abpoa.h"

// Nucleotide encoding table: ACGT -> 0123
unsigned char nt4_table[256] = {
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4, // A=0, C=1, G=2
    4,4,4,4, 3,3,4,4, 4,4,4,4, 4,4,4,4, // T=U=3
    4,0,4,1, 4,4,4,2, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 3,3,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4,
    4,4,4,4, 4,4,4,4, 4,4,4,4, 4,4,4,4
};

const char nt256_table[256] = {
    'A','C','G','T', 'N','-','N','N', 'N','N','N','N', 'N','N','N','N',
    // ... (maps encoded values back to characters)
};

int main() {
    int i, j, n_seqs = 4;
    char *seqs[] = {
        "CGTCAATCTATCGAAGCATACGCGGGCAGAGCC",
        "CCACGTCAATCTATCGAAGCATACGCGGCAGCC",
        "CGTCAATCTATCGAAGCATACGCGGCAGAGCCC",
        "CGTCAATGCTAGTCGAAGCAGCTGCGGCAGAGCC"
    };

    // Initialize
    abpoa_t *ab = abpoa_init();
    abpoa_para_t *abpt = abpoa_init_para();
    abpt->out_msa = 1;
    abpt->out_cons = 1;
    abpt->max_n_cons = 2;
    abpoa_post_set_para(abpt);

    // Prepare sequence data
    int *seq_lens = malloc(sizeof(int) * n_seqs);
    uint8_t **bseqs = malloc(sizeof(uint8_t*) * n_seqs);

    for (i = 0; i < n_seqs; i++) {
        seq_lens[i] = strlen(seqs[i]);
        bseqs[i] = malloc(sizeof(uint8_t) * seq_lens[i]);
        for (j = 0; j < seq_lens[i]; j++) {
            bseqs[i][j] = nt4_table[(int)seqs[i][j]];
        }
    }

    // Perform MSA - output directly to stdout
    abpoa_msa(ab, abpt, n_seqs, NULL, seq_lens, bseqs, NULL, stdout);

    // Access results programmatically
    abpoa_cons_t *abc = ab->abc;
    printf("\n=== Programmatic access ===\n");
    printf("MSA length: %d\n", abc->msa_len);
    printf("Number of consensus: %d\n", abc->n_cons);

    // Print MSA
    for (i = 0; i < abc->n_seq; i++) {
        printf(">Seq_%d\n", i + 1);
        for (j = 0; j < abc->msa_len; j++) {
            printf("%c", nt256_table[abc->msa_base[i][j]]);
        }
        printf("\n");
    }

    // Print consensus sequences
    for (i = 0; i < abc->n_cons; i++) {
        printf(">Consensus_%d (length: %d)\n", i + 1, abc->cons_len[i]);
        for (j = 0; j < abc->cons_len[i]; j++) {
            printf("%c", nt256_table[abc->cons_base[i][j]]);
        }
        printf("\n");
    }

    // Cleanup
    for (i = 0; i < n_seqs; i++) free(bseqs[i]);
    free(bseqs);
    free(seq_lens);
    abpoa_free(ab);
    abpoa_free_para(abpt);

    return 0;
}

```

--------------------------------

### Align Sequence to Existing Graph (MSA Input)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Aligns a sequence to an existing graph provided in MSA (FASTA) format. Gaps are indicated by '-'.

```bash
abpoa -i in.msa seq.fa -r1 > out.msa
```

--------------------------------

### Generate Default Consensus Sequence

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates a consensus sequence from a FASTA file using the default 'heaviest bundling' method.

```bash
abpoa seq.fa > cons.fa
```

--------------------------------

### Generate Graph Information in GFA Format

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates graph information in GFA format. Use '-r3' for basic GFA output.

```bash
abpoa seq.fa -r3 > out.gfa
```

--------------------------------

### pyabpoa.msa_aligner

Source: https://context7.com/yangao07/abpoa/llms.txt

Initializes the alignment engine with custom parameters for sequence processing.

```APIDOC
## Class: pyabpoa.msa_aligner

### Description
Initializes the alignment engine for performing multiple sequence alignment (MSA) and consensus calling.

### Parameters
- **aln_mode** (str) - Optional - Alignment mode: 'g' (global), 'l' (local), 'e' (extension).
- **is_aa** (bool) - Optional - Set True for amino acid sequences.
- **match** (int) - Optional - Match score.
- **mismatch** (int) - Optional - Mismatch penalty.
- **gap_open1** (int) - Optional - First gap opening penalty.
- **gap_ext1** (int) - Optional - First gap extension penalty.
- **gap_open2** (int) - Optional - Second gap opening penalty (convex).
- **gap_ext2** (int) - Optional - Second gap extension penalty (convex).
- **extra_b** (int) - Optional - Adaptive banding parameter.
- **extra_f** (float) - Optional - Banding factor.
- **cons_algrm** (str) - Optional - Consensus algorithm: 'HB' (heaviest bundling), 'MF' (most frequent).

### Request Example
```python
aligner = pa.msa_aligner(aln_mode='g', match=2, mismatch=4)
```
```

--------------------------------

### Generate Consensus Sequence (Most Frequent Bases)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates a consensus sequence using the 'most frequent bases' method. Use the '-a1' flag.

```bash
abpoa seq.fa -a1 > cons.fa
```

--------------------------------

### Align Sequence to Existing Graph (GFA Input)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Aligns a sequence to an existing graph provided in GFA format. Requires 'S' and 'P' lines in the GFA file.

```bash
abpoa -i in.gfa seq.fa -r3 > out.gfa
```

--------------------------------

### Visualize Alignment Graphs in Python

Source: https://context7.com/yangao07/abpoa/llms.txt

Generates visual representations of the partial order alignment graph, requiring the graphviz package.

```python
import pyabpoa as pa

aligner = pa.msa_aligner()

seqs = [
    'ACGTACGT',
    'ACGTTACGT',
    'ACGTACGT',
    'ACGAACGT'
]

# Generate MSA with graph visualization
result = aligner.msa(
    seqs,
    out_cons=True,
    out_msa=True,
    out_pog='alignment_graph.png'  # or 'alignment_graph.pdf'
)

# Graph is saved to the specified file
# Nodes contain base and ID, edges show weights
print("Graph saved to alignment_graph.png")
```

--------------------------------

### Instantiate msa_aligner

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Constructs a multiple sequence alignment handler. The `aln_mode` parameter controls the alignment type (global, local, or extension).

```python
pyabpoa.msa_aligner(aln_mode='g', ...)
```

--------------------------------

### Generate Multiple Consensus Sequences

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates multiple consensus sequences for files containing 2 or 3 alleles. Use '-d2' for two and '-d3' for three.

```bash
abpoa heter.fa -d2 > 2cons.fa
abpoa 3alleles.fa -d3 > 3cons.fa
```

--------------------------------

### Generate Multiple Consensus Sequences in Python

Source: https://context7.com/yangao07/abpoa/llms.txt

Cluster sequences to generate multiple consensus outputs for heterozygous or diploid data.

```python
import pyabpoa as pa

aligner = pa.msa_aligner()

# Heterozygous sequences (two distinct alleles)
seqs = [
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATAAAAAAAAAAAAAAAAAAACGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT',
    'CGATCGATCGATCGATGCATGCATCGATGCATCGATCGATGCATGCAT'
]
```

--------------------------------

### Generate Alignment Graph Plot

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates a plot of the alignment graph and saves it as a PNG file. Requires the '-g' option.

```bash
abpoa seq.fa -g poa.png > cons.fa
```

--------------------------------

### Perform Incremental MSA in Python

Source: https://context7.com/yangao07/abpoa/llms.txt

Adds new sequences to an existing alignment graph or loads from a file to avoid full recomputation.

```python
import pyabpoa as pa

# Initial sequences
seqs = [
    'CCGAAGA',
    'CCGAACTCGA',
    'CCCGGAAGA',
    'CCGAAGA'
]

# New sequences to add incrementally
new_seqs = [
    'CCAGA',
    'CCGAAAGA'
]

# Create aligner and perform initial MSA
aligner = pa.msa_aligner()

# Method 1: Using msa_align + msa_add + msa_output
aligner.msa_align(seqs, out_cons=True, out_msa=True)
aligner.msa_add(new_seqs)
result = aligner.msa_output()

print("Incremental MSA result:")
result.print_msa()
for seq in result.cons_seq:
    print(f"Consensus: {seq}")

# Method 2: Load from existing graph/MSA file
aligner2 = pa.msa_aligner()
result2 = aligner2.msa(
    new_seqs,
    out_cons=True,
    out_msa=True,
    incr_fn='existing.gfa'  # or 'existing.msa' FASTA file
)
```

--------------------------------

### Incrementally add sequences to MSA

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Shows how to incrementally add new sequences to an existing alignment using pyabpoa. This involves creating a new aligner, performing an initial alignment, adding new sequences, and then outputting the updated alignment.

```python
# incrementally add new seqs
new_seqs=[
'CCAGA',
'CCGAAAGA'
]
b = pa.msa_aligner()
b.msa_align(seqs, out_cons=True, out_msa=True)
b.msa_add(new_seqs)
b_res = b.msa_output()
b_res.print_msa()
```

--------------------------------

### Generate GFA with Consensus Path

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates GFA format output that includes the consensus sequence as a path. Use '-r4'.

```bash
abpoa seq.fa -r4 > out.gfa
```

--------------------------------

### Generate Multiple Consensus Sequences

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Use the -d/--max-num-cons option to generate two or more consensus sequences for diploid input. The output includes sequences named 'Consensus_sequence_1', 'Consensus_sequence_2', etc.

```bash
abpoa heter.fa -d2
```

```text
>Consensus_sequence_1
CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
>Consensus_sequence_2
CCATTCCCACCATCCTTACCATCAACATCACCATCCCCACCATCCCCAACACCATTCCCACCATCCCTACCATCACCATCACCATCCCCACCAACATCCCCACCACCATCCTCACTACCATCCCCACCACCATTTCCACCATTCCCACCACAGTCACCATCACCCCCACCATCCCCATCATCATCCGCACCATCCCCACCATCCCCACCACCATCTCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCCCATTACCATCCCCACCACCATCCCCATTACCATCCCCACCACCATTTCCACCATTCCCACCATCATCCCCACCACCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCATCCCCACCGCCATCCTCGTTACCATCCCCACCACCTTTTCCACCATTCCCACCATCTCCAACACCTCCCCCACCATCATCCCCACCATCCCCACCACCTTCTCCACCATCATTCTCACCATCCCCACCACCATCTCCACCACCATTCTCACCATCTCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCAACATCCCCACCATCCCCACCCCCATGCCCACCATCATCCCCACCATCC
```

--------------------------------

### Generate Consensus for Amino Acid Sequences

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates a consensus sequence for amino acid sequences using a specified scoring matrix (e.g., BLOSUM62).

```bash
abpoa -c -t BLOSUM62.mtx input_aa.fa > output_aa_cons.fa
```

--------------------------------

### Add new sequences incrementally

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Adds new sequences to an ongoing alignment process. This method should be called after `msa_align` and before `msa_output`.

```python
pyabpoa.msa_aligner.msa_add(new_seqs)
```

--------------------------------

### Generate Row-Column Multiple Sequence Alignment

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Generates a multiple sequence alignment in FASTA format. Use '-r1' for standard MSA and '-r2' for MSA with consensus.

```bash
abpoa seq.fa -r1 > out.msa
abpoa seq.fa -r2 > out_cons.msa
```

--------------------------------

### Output Full Graph Information (GFA format)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Outputs the final alignment graph in GFA format. Segment lines ('S') represent nodes, link lines ('L') represent edges, and path lines ('P') describe original sequences and consensus. Header lines ('H') contain node ('NS') and edge ('NL') counts.

```text
H	VN:Z:1.0	NS:i:10	NL:i:15
S	1	*	LN:i:10
L	1	+	2	+	10
...
```

--------------------------------

### Perform MSA with Python API

Source: https://context7.com/yangao07/abpoa/llms.txt

Use the msa_aligner class to configure alignment parameters and process sequences in Python.

```python
import pyabpoa as pa

# Create aligner with default parameters
aligner = pa.msa_aligner()

# Create aligner with custom parameters
aligner = pa.msa_aligner(
    aln_mode='g',        # 'g': global, 'l': local, 'e': extension
    is_aa=False,         # Set True for amino acid sequences
    match=2,             # Match score
    mismatch=4,          # Mismatch penalty
    gap_open1=4,         # First gap opening penalty
    gap_ext1=2,          # First gap extension penalty
    gap_open2=24,        # Second gap opening penalty (convex)
    gap_ext2=1,          # Second gap extension penalty (convex)
    extra_b=10,          # Adaptive banding parameter (-1 to disable)
    extra_f=0.01,        # Banding factor: width = extra_b + extra_f * L
    cons_algrm='HB'      # 'HB': heaviest bundling, 'MF': most frequent
)

# Perform MSA on a list of sequences
seqs = [
    'CGTCAATCTATCGAAGCATACGCGGGCAGAGCCGAAGACCTCGGCAATCCA',
    'CCACGTCAATCTATCGAAGCATACGCGGCAGCCGAACTCGACCTCGGCAATCAC',
    'CGTCAATCTATCGAAGCATACGCGGCAGAGCCCGGAAGACCTCGGCAATCAC',
    'CGTCAATGCTAGTCGAAGCAGCTGCGGCAGAGCCGAAGACCTCGGCAATCAC'
]

result = aligner.msa(seqs, out_cons=True, out_msa=True)

# Access results
print(f"Number of sequences: {result.n_seq}")
print(f"Number of consensus: {result.n_cons}")
print(f"MSA length: {result.msa_len}")

for i, cons in enumerate(result.cons_seq):
    print(f">Consensus_{i+1}\n{cons}")

# Print row-column MSA
result.print_msa()
```

--------------------------------

### Print RC-MSA

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Prints the Row-Column Multiple Sequence Alignment (RC-MSA) to the console. This is a method of the `msa_result` object.

```python
pyabpoa.msa_result().print_msa()
```

--------------------------------

### Output MSA results

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Retrieves the results of the multiple sequence alignment, including consensus sequences and the alignment itself. This method must be called after `msa_align` and `msa_add`.

```python
pyabpoa.msa_aligner.msa_output()
```

--------------------------------

### Class pyabpoa.msa_result

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Contains the output data from the alignment process, including consensus sequences and the RC-MSA.

```APIDOC
## Class pyabpoa.msa_result

### Description
Stores and provides access to the results of the multiple sequence alignment.

### Properties
- **n_seq** (int) - Number of input sequences.
- **n_cons** (int) - Number of consensus sequences.
- **clu_n_seq** (array) - Cluster sizes.
- **cons_len** (array) - Lengths of consensus sequences.
- **cons_seq** (array) - The consensus sequences.
- **cons_cov** (array) - Coverage for each base.
- **msa_len** (int) - Size of each row in RC-MSA.
- **msa_seq** (array) - The RC-MSA alignment strings.

### Methods
- **print_msa()** - Prints the RC-MSA to the screen.
```

--------------------------------

### Method pyabpoa.msa_aligner.msa

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Performs multiple sequence alignment on a list of sequences and returns an msa_result object.

```APIDOC
## Method pyabpoa.msa_aligner.msa

### Description
Executes the MSA process and returns the alignment results.

### Parameters
- **seqs** (list) - Required - List of input sequences.
- **out_cons** (bool) - Required - Generate consensus sequence.
- **out_msa** (bool) - Required - Generate RC-MSA.
- **max_n_cons** (int) - Optional - Max number of consensus sequences. Default: 1.
- **min_freq** (float) - Optional - Minimum frequency for consensus. Default: 0.3.
- **out_pog** (str) - Optional - File path to save alignment graph plot.
- **incr_fn** (str) - Optional - Existing graph or MSA file for incremental alignment.

### Response
- **msa_result** (object) - An object containing the alignment results.
```

--------------------------------

### Perform MSA with msa method

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

Performs multiple sequence alignment using the `msa` method of the `msa_aligner` class. It takes a list of sequences and boolean flags to control output generation.

```python
pyabpoa.msa_aligner.msa(seqs, out_cons, out_msa, out_pog='', incr_fn='')
```

--------------------------------

### Generate Row-Column Multiple Sequence Alignment (RC-MSA)

Source: https://github.com/yangao07/abpoa/blob/main/README.md

Outputs the row-column multiple sequence alignment (RC-MSA) of all aligned sequences in FASTA format. Alignment gaps are represented by '-'.

```text
>1
ACGTGTACA-GTTGAC
>2
A-G-GTACACGTT-AC
>3
A-GTGT-CACGTTGAC
>4
ACGTGTACA--TTGAC
```

--------------------------------

### Class pyabpoa.msa_aligner

Source: https://github.com/yangao07/abpoa/blob/main/python/README.md

The msa_aligner class is the primary handler for configuring and performing multiple sequence alignment.

```APIDOC
## Class pyabpoa.msa_aligner

### Description
Initializes the alignment handler with specific parameters for scoring and gap penalties.

### Parameters
- **aln_mode** (str) - Optional - Alignment mode: 'g' (global), 'l' (local), 'e' (extension). Default: 'g'.
- **is_aa** (bool) - Optional - True if input is amino acid sequence. Default: False.
- **match** (int) - Optional - Match score. Default: 2.
- **mismatch** (int) - Optional - Mismatch penalty. Default: 4.
- **score_matrix** (str) - Optional - Scoring matrix file path.
- **gap_open1** (int) - Optional - First gap opening penalty. Default: 4.
- **gap_ext1** (int) - Optional - First gap extension penalty. Default: 2.
- **gap_open2** (int) - Optional - Second gap opening penalty. Default: 24.
- **gap_ext2** (int) - Optional - Second gap extension penalty. Default: 1.
- **extra_b** (int) - Optional - First adaptive banding parameter. Default: 10.
- **extra_f** (float) - Optional - Second adaptive banding parameter. Default: 0.01.
- **cons_algrm** (str) - Optional - Consensus algorithm: 'HB' (heaviest bundling), 'MF' (most frequent). Default: 'HB'.
```
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