---
name: "Bio::Matrix::IO::mlagan"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Matrix::IO::mlagan"
---

# Bio::Matrix::IO::mlagan(3pm)

A parser for the mlagan substitution matrix

## NAME

Bio::Matrix::IO::mlagan - A parser for the mlagan substitution matrix

## SYNOPSIS

```
  use Bio::Matrix::IO;
  my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
                                   -file   => 'nucmatrix.txt');
  my $matrix = $parser->next_matrix;
  my $gap_open = $parser->gap_open;
  my $gap_continue = $parser->gap_continue;
```

## DESCRIPTION

Use to read in and write out substitution matrix files suitable for use by mlagan.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Sendu Bala

Email bix@sendu.me.uk

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### new

```
 Title   : new
 Usage   : my $obj = Bio::Matrix::IO::mlagan->new();
 Function: Builds a new Bio::Matrix::IO::mlagan object
 Returns : an instance of Bio::Matrix::IO::mlagan
 Args    :
```

### next\_matrix

```
 Title   : next_matrix
 Usage   : my $matrix = $obj->next_matrix();
 Function: parses a matrix file
 Returns : L<Bio::Matrix::Mlagan>
 Args    : none
```

### write\_matrix

```
 Title   : write_matrix
 Usage   : $obj->write_matrix($matrix)
 Function: Write out a matrix in mlagan format
 Returns : n/a
 Args    : L<Bio::Matrix::Generic>
```