---
name: "Bio::AlignIO::msf"
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::AlignIO::msf"
---

# Bio::AlignIO::msf(3pm)

msf sequence input/output stream

## NAME

Bio::AlignIO::msf - msf sequence input/output stream

## SYNOPSIS

Do not use this module directly.  Use it via the Bio::AlignIO class.

## DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from msf flat file databases.

## FEEDBACK

### 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 the bugs and their resolution.  Bug reports can be submitted via the web:

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

## AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

## APPENDIX

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

### next\_aln

```
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream. Tries to read *all* MSF
           It reads all non whitespace characters in the alignment
           area. For MSFs with weird gaps (eg ~~~) map them by using
           $aln->map_chars('~','-')
 Returns : Bio::Align::AlignI object
 Args    : NONE
```

### write\_aln

```
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in MSF format
           Sequence type of the alignment is determined by the first sequence.
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object
```