Calculate various summary statistics on a multiple sequence alignment
Project description
# AMAS
Calculate various summary statistics on a multiple sequence alignment
## Usage
AMAS can be run from the command line:
```shell
python AMAS.py <input_file> <format> <alphabet>
```
The supported formats are `fasta`, `phylip`, `nexus`, `phylip-int`, and `nexus-int`. The alphabets are `aa` or `dna`.
Also, AMAS can be imported from other Python modules:
```python
>>> from amas import AMAS
>>> in_file = 'fasta1.fas'
>>> in_format = 'fasta'
>>> data_type = 'dna'
>>> aln = AMAS.DNAAlignment(in_file, in_format, data_type)
>>> aln.summarize_alignment()
['fasta1.fas', '10', '100', '1000', '1', '0.1', '2', '0.02', '1', '0.01']
```
Calculate various summary statistics on a multiple sequence alignment
## Usage
AMAS can be run from the command line:
```shell
python AMAS.py <input_file> <format> <alphabet>
```
The supported formats are `fasta`, `phylip`, `nexus`, `phylip-int`, and `nexus-int`. The alphabets are `aa` or `dna`.
Also, AMAS can be imported from other Python modules:
```python
>>> from amas import AMAS
>>> in_file = 'fasta1.fas'
>>> in_format = 'fasta'
>>> data_type = 'dna'
>>> aln = AMAS.DNAAlignment(in_file, in_format, data_type)
>>> aln.summarize_alignment()
['fasta1.fas', '10', '100', '1000', '1', '0.1', '2', '0.02', '1', '0.01']
```
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